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Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex with phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% PEG-smear (PEG3350 & PEG MME5K), 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.96 α = 90 b = 73.09 β = 90 c = 81.29 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 2009-12-13 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) 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 1.9 36.54 100 0.049 15.8 4.7 34056 33999 34.7
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) 1.9 2 100 0.669 2.2 4.6 4896
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.9 36.54 33999 32302 1697 99.98 0.18524 0.18299 0.1808 0.22813 0.2228 RANDOM 38.081
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] 1.05 -0.12 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.505 r_dihedral_angle_4_deg 22.623 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.672 r_angle_other_deg 0.886 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.505 r_dihedral_angle_4_deg 22.623 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.672 r_angle_other_deg 0.886 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3039 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 64
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling