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Crystal Structure of Chlamydia trachomatis Glyceraldehyde 3-phosphate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 25% PEG 2000 MME, 0.1 M Hepes, pH 7.5;
prior to crystallization the protein (at 30 mg/ml) was incubated with 1 mM NAD
Crystal Properties Matthews coefficient Solvent content 1.98 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.603 α = 90 b = 104.053 β = 97.48 c = 86.473 γ = 90
Symmetry Space Group P 1 21 1
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 2016-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 66.26 93.2 0.076 0.089 0.045 0.997 10.2 3.3 173217 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 93 0.626 0.742 0.388 0.679 3.3
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 4QX6 1.5 66.26 164358 8819 92.91 0.1713 0.1703 0.1708 0.1885 0.1895 RANDOM 17.1
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] -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 10.759 r_dihedral_angle_1_deg 7.071 r_angle_other_deg 1.377 r_angle_refined_deg 1.364 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 10.759 r_dihedral_angle_1_deg 7.071 r_angle_other_deg 1.377 r_angle_refined_deg 1.364 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10164 Nucleic Acid Atoms Solvent Atoms 1230 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing