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Crystal structure of human phosphoribosyl pyrophosphate synthetase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HCR PDB ENTRY 2HCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 295 2.1M ammonium sulfate, 0.1M sodium acetate, 10% (v/v) glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.18 α = 90 b = 169.18 β = 90 c = 61.84 γ = 120
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 MAR scanner 345 mm plate 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54179
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 2.6 42.295 91.2 0.065 0.065 8.5 1.4 18873 18518 50.4
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) 2.6 2.74 88.5 0.345 0.345 1.8 1.4 2623
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 2HCR 2.6 30 18508 17561 947 91.19 0.21649 0.21649 0.2157 0.21 0.23133 0.2264 RANDOM 33.116
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] 0.79 0.39 0.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_3_deg 18.781 r_dihedral_angle_4_deg 12.884 r_dihedral_angle_1_deg 5.119 r_scangle_it 1.243 r_angle_refined_deg 1.08 r_scbond_it 0.826 r_mcangle_it 0.649 r_mcbond_it 0.49 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_3_deg 18.781 r_dihedral_angle_4_deg 12.884 r_dihedral_angle_1_deg 5.119 r_scangle_it 1.243 r_angle_refined_deg 1.08 r_scbond_it 0.826 r_mcangle_it 0.649 r_mcbond_it 0.49 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4592 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 30
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling