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Y92C catalytic residue mutant of Phosphoglycerate Mutase from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 35% PEG 1000, 0.1 M HEPES pH 7.2, 0.1 M KSCN, 5 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.062 α = 90 b = 76.12 β = 99.68 c = 101.68 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 325 mm CCD 2007-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.91837 SSRL BL9-1
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 2.08 50 99.5 0.055 10.5 2.6 64085 3 45
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 2.08 2.15 99.8 0.599 1.22 2.5 6390
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 1xq9 2.08 31.46 64066 3209 99.13 0.198 0.196 0.2094 0.236 0.2434 RANDOM 26.78
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] -0.05 -0.11 -0.07 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.441 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_4_deg 9.136 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.164 r_scbond_it 2.084 r_mcangle_it 1.75 r_mcbond_it 1.056 r_angle_refined_deg 0.93 r_angle_other_deg 0.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.441 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_4_deg 9.136 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.164 r_scbond_it 2.084 r_mcangle_it 1.75 r_mcbond_it 1.056 r_angle_refined_deg 0.93 r_angle_other_deg 0.791 r_mcbond_other 0.284 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7485 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing