☰ Navigation Tabs
Crystal structure of human B type phosphoglycerate mutase H11 phosphorylated form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YFK PDB ENTRY 1YFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG3350, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.36 α = 90 b = 81.174 β = 90 c = 90.381 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 180 CCD ADSC QUANTUM 315 2011-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 60.478 100 72475 72475 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 100
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 PDB ENTRY 1YFK 1.65 60.39 65490 3493 99.86 0.18647 0.18502 0.1835 0.21382 0.2112 RANDOM 28.291
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] 2.29 -0.44 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_4_deg 12.937 r_dihedral_angle_1_deg 5.951 r_angle_refined_deg 2.471 r_chiral_restr 0.303 r_bond_refined_d 0.025 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_4_deg 12.937 r_dihedral_angle_1_deg 5.951 r_angle_refined_deg 2.471 r_chiral_restr 0.303 r_bond_refined_d 0.025 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3844 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHASES phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 data collection