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Structure of phosphoheptose isomerase GmhA from Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M TRIS-HCL pH 8.5, 0.2M magnesium chloride, 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.02 39.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.36 α = 90 b = 130.15 β = 90 c = 47.15 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 CCD RAYONIX MX300-HS 2015-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.37 85.91 95.8 0.134 0.996 9.34 3.7 28174 -3 41.167
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 2.37 2.43 97.8 1.032 1.71
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 3BJZ 2.37 85.91 26786 1405 95.86 0.2101 0.2071 0.2132 0.2667 0.2669 RANDOM 37.172
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] 1.3 -2.2 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_4_deg 16.676 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 5.165 r_mcangle_it 2.432 r_mcbond_it 1.478 r_mcbond_other 1.477 r_angle_refined_deg 1.224 r_angle_other_deg 0.93 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_4_deg 16.676 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 5.165 r_mcangle_it 2.432 r_mcbond_it 1.478 r_mcbond_other 1.477 r_angle_refined_deg 1.224 r_angle_other_deg 0.93 r_chiral_restr 0.069 r_bond_refined_d 0.009 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 5411 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction