3PZY

Crystal structure of Molybdopterin biosynthesis mog protein from Mycobacterium paratuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OI9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6290Internal tracking number 217822A1. PACT screen condition A1: SPG buffer, pH 4, 25% PEG1500, with protein (MypaA.00778.b.A1 PW29403) at 24.39 mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.244.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.65α = 90
b = 68.65β = 90
c = 52.83γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976504ALS5.0.3

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
11.819.7599.30.04224.395.488891323613146-333.133
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)
11.81.8599.60.5193.35.544979960

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3OI91.819.75132361312864699.180.1950.1950.1930.228RANDOM26.401
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]
0.70.350.7-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.919
r_dihedral_angle_3_deg13.59
r_dihedral_angle_4_deg12.212
r_dihedral_angle_1_deg5.258
r_scangle_it4.029
r_scbond_it2.425
r_angle_refined_deg1.566
r_mcangle_it1.507
r_angle_other_deg0.989
r_mcbond_it0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.919
r_dihedral_angle_3_deg13.59
r_dihedral_angle_4_deg12.212
r_dihedral_angle_1_deg5.258
r_scangle_it4.029
r_scbond_it2.425
r_angle_refined_deg1.566
r_mcangle_it1.507
r_angle_other_deg0.989
r_mcbond_it0.922
r_mcbond_other0.274
r_chiral_restr0.092
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1024
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms5

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
REFMACphasing