☰ Navigation Tabs
Crystal structure of phosphoglycerate mutase from Cryptosporidium parvum, cgd7_4270
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQ9 PDB entry 1XQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 273 25% PEG 3350, 0.2 M NH4OAc, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.248 α = 90 b = 158.365 β = 90 c = 140.249 γ = 90
Symmetry Space Group C 2 2 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 2008-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.01 50 100 0.075 0.046 9.6 7.2 39125 39125 35.9
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 2.08 100 0.796 0.796 2.32 6.9 3847
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XQ9 2.01 40.5 39074 39074 1958 99.74 0.233 0.233 0.231 0.3015 0.256 0.3175 RANDOM 35.774
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] 1.8 -0.25 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_1_deg 5.92 r_scangle_it 1.504 r_angle_refined_deg 1.141 r_scbond_it 1.02 r_mcangle_it 0.647 r_mcbond_it 0.384 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_1_deg 5.92 r_scangle_it 1.504 r_angle_refined_deg 1.141 r_scbond_it 1.02 r_mcangle_it 0.647 r_mcbond_it 0.384 r_nbtor_refined 0.299 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3641 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction