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Crystal structure of a phosphoglycerate mutase gpm1 from Mycobacterium leprae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MyleA.00184.a.A1 PS01437 at 18.1 mg/mL against JCSG+ A8 0.2 M ammonium formate, 20% PEG 3350 supplemented with 15% PEG 400 as cryo-protectant, crystal tracking ID 233299a8, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.23 61.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.31 α = 90 b = 80.31 β = 90 c = 119.33 γ = 90
Symmetry Space Group P 42 2 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 RIGAKU SATURN 944+ 2012-04-11 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 2.45 50 99.8 0.075 21 7 15013 14961 -3 45.491
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 2.45 2.51 99.7 0.529 4
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 2.45 50 14960 755 99.81 0.1976 0.1958 0.1959 0.2348 0.234 RANDOM 39.0887
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] 0.97 0.97 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 16.582 r_dihedral_angle_1_deg 6.159 r_angle_refined_deg 1.497 r_angle_other_deg 1.019 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 16.582 r_dihedral_angle_1_deg 6.159 r_angle_refined_deg 1.497 r_angle_other_deg 1.019 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1861 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction