2Q5W

The X-ray Crystal Structure of Molybdopterin Synthase from Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FM0PDB ENTRY 1FM0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.32952.0 M Sodium Formate, 0.1 M Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties
Matthews coefficientSolvent content
2.5651.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.922α = 90
b = 45.754β = 93.36
c = 41.772γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.1NSLSX26C

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
125094.80.033293.316442
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)
122.0771.40.0652.1

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 1FM02301554882494.950.150870.148660.19321RANDOM24.645
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]
-1.020.232.02-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.473
r_dihedral_angle_4_deg22.417
r_dihedral_angle_3_deg13.586
r_dihedral_angle_1_deg6.771
r_scangle_it3.638
r_scbond_it2.598
r_angle_refined_deg1.551
r_mcangle_it1.308
r_mcbond_it1.162
r_angle_other_deg0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.473
r_dihedral_angle_4_deg22.417
r_dihedral_angle_3_deg13.586
r_dihedral_angle_1_deg6.771
r_scangle_it3.638
r_scbond_it2.598
r_angle_refined_deg1.551
r_mcangle_it1.308
r_mcbond_it1.162
r_angle_other_deg0.83
r_symmetry_hbond_refined0.275
r_symmetry_vdw_refined0.262
r_mcbond_other0.252
r_nbd_refined0.217
r_symmetry_vdw_other0.192
r_xyhbond_nbd_refined0.185
r_nbd_other0.183
r_nbtor_refined0.181
r_chiral_restr0.103
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1761
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
MOLREPphasing