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Crystal structure of molybdenum cofactor synthesis domain from Mycobacterium avium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G4R 2g4r molecule a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 29.9 mg/mL MyavA.00778.b.A1 PW28925 against EBS PACT screen condition A8, 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217062a8, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.03 α = 90 b = 68.03 β = 90 c = 53.17 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ 2010-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 50 99.6 0.046 19.07 3.9 10314 10275 -3 33.744
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.6 0.441 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2g4r molecule a 1.95 50 10254 493 99.43 0.1987 0.1962 0.1972 0.2446 0.2347 RANDOM 40.3835
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 11.838 r_dihedral_angle_3_deg 11.531 r_dihedral_angle_1_deg 4.62 r_scangle_it 3.445 r_scbond_it 1.985 r_angle_refined_deg 1.361 r_mcangle_it 1.262 r_mcbond_it 0.713 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 11.838 r_dihedral_angle_3_deg 11.531 r_dihedral_angle_1_deg 4.62 r_scangle_it 3.445 r_scbond_it 1.985 r_angle_refined_deg 1.361 r_mcangle_it 1.262 r_mcbond_it 0.713 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1032 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction