2VVR

Crystal structure of the H99N mutant of ribose-5-phosphate isomerase B from E. coli soaked with ribose 5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NN4PDB ENTRY 1NN4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3350, 0.1 M MES PH6
Crystal Properties
Matthews coefficientSolvent content
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.701α = 90
b = 51.862β = 115.55
c = 207.209γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2007-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.140.4999.90.1114.13.6506355.819.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2199.90.175.83.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NN42.14048057257499.90.190.1880.237RANDOM13.77
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]
-0.43-0.19-0.610.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.444
r_dihedral_angle_4_deg19.164
r_dihedral_angle_3_deg12.654
r_dihedral_angle_1_deg5.589
r_scangle_it2.571
r_scbond_it1.786
r_angle_refined_deg1.175
r_mcangle_it0.999
r_angle_other_deg0.95
r_mcbond_it0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.444
r_dihedral_angle_4_deg19.164
r_dihedral_angle_3_deg12.654
r_dihedral_angle_1_deg5.589
r_scangle_it2.571
r_scbond_it1.786
r_angle_refined_deg1.175
r_mcangle_it0.999
r_angle_other_deg0.95
r_mcbond_it0.87
r_symmetry_vdw_other0.212
r_nbd_refined0.196
r_nbd_other0.184
r_nbtor_refined0.171
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.153
r_mcbond_other0.128
r_xyhbond_nbd_refined0.126
r_nbtor_other0.083
r_chiral_restr0.068
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6621
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing