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Crystal structure oh human phosphoglycerate mutase family member 5 (PGAM5)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG-smear (PEG3350 & PEG MME5K), 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.602 α = 90 b = 70.946 β = 90 c = 81.476 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2009-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 29.48 99.5 0.053 0.053 16.7 4.8 45741 45512 24.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 97.6 0.644 0.724 2.2 4.6 6408
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 SIRAS THROUGHOUT 1.7 29.48 45419 2283 99.4 0.17 0.168 0.1721 0.203 0.2 RANDOM 27.699
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] 0.63 -0.38 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_4_deg 21.448 r_dihedral_angle_3_deg 13.686 r_dihedral_angle_1_deg 5.866 r_angle_refined_deg 1.504 r_angle_other_deg 0.915 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_4_deg 21.448 r_dihedral_angle_3_deg 13.686 r_dihedral_angle_1_deg 5.866 r_angle_refined_deg 1.504 r_angle_other_deg 0.915 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3014 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 92
Software Software Software Name Purpose SCALA data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction