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4-hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298.15 pH 4.5, 100mM Na-acetate/acetic acid, 200mM lithium sulfate, 50% (v/v) PEG 400, 0.5uL of 100% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.14 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 356.98 α = 90 b = 70.4 β = 90 c = 75.81 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-11-10 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.73 - 1.85 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.69 24.88 98 0.99 7.49 13.16 53788 51.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.75 92.2 0.27 0.59 11.77
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 24.88 41150 2992 91.43 0.23921 0.23618 0.2389 0.2801 0.2785 RANDOM 65.844
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] 1.92 -3.2 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.281 r_long_range_B_refined 8.963 r_long_range_B_other 8.957 r_dihedral_angle_1_deg 7.672 r_mcangle_it 4.615 r_mcangle_other 4.615 r_scangle_other 4.387 r_mcbond_it 2.741 r_mcbond_other 2.741 r_scbond_it 2.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.281 r_long_range_B_refined 8.963 r_long_range_B_other 8.957 r_dihedral_angle_1_deg 7.672 r_mcangle_it 4.615 r_mcangle_other 4.615 r_scangle_other 4.387 r_mcbond_it 2.741 r_mcbond_other 2.741 r_scbond_it 2.581 r_scbond_other 2.576 r_angle_refined_deg 1.304 r_angle_other_deg 0.458 r_chiral_restr 0.12 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9479 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing