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Crystal structure of phosphoglycerate mutase from Staphylococcus aureus in 2-phosphoglyceric acid bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 298 0.2M NaCl, Bis-tris, 25%(w/v) PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.639 α = 90 b = 83.206 β = 90 c = 89.073 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++ Varimax (osmic mirror) 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.01 60.804 99.1 0.1 19.7 7.1 37033 37033
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 2.01 2.11 95.3 0.49 0.49 1.6 6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4MY4 2.01 19.64 35134 1848 99 0.17003 0.16767 0.21593 0.181 RANDOM 19.521
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] 0.27 0.74 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_4_deg 18.95 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_1_deg 6.758 r_angle_refined_deg 1.992 r_angle_other_deg 1.033 r_chiral_restr 0.176 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_4_deg 18.95 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_1_deg 6.758 r_angle_refined_deg 1.992 r_angle_other_deg 1.033 r_chiral_restr 0.176 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3955 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 21
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Structure data collection XDS data reduction