1SVD | pdb_00001svd

The structure of Halothiobacillus neapolitanus RuBisCo


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RBLpdb entry 1rbl

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8298ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6853.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.066α = 90
b = 157.066β = 90
c = 107.609γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Double Crystal Si(111)2003-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.1271ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8900.09119.49.46213862138
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.861000.3558.710.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUTpdb entry 1rbl1.887.715898458984309599.950.146080.145020.160.165740.18RANDOM11.186
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.490.49-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.893
r_scangle_it4.207
r_scbond_it2.665
r_mcangle_it1.759
r_angle_refined_deg1.519
r_mcbond_it0.945
r_angle_other_deg0.91
r_symmetry_hbond_refined0.307
r_symmetry_vdw_other0.304
r_nbd_other0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.893
r_scangle_it4.207
r_scbond_it2.665
r_mcangle_it1.759
r_angle_refined_deg1.519
r_mcbond_it0.945
r_angle_other_deg0.91
r_symmetry_hbond_refined0.307
r_symmetry_vdw_other0.304
r_nbd_other0.246
r_symmetry_vdw_refined0.223
r_nbd_refined0.209
r_xyhbond_nbd_refined0.124
r_chiral_restr0.099
r_nbtor_other0.085
r_gen_planes_other0.022
r_bond_refined_d0.015
r_gen_planes_refined0.015
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4369
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing