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Crystal structure of mutant rabbit PRP 121-230 (S170N/S174N)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O79 PDB ENTRY 3O79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100mM SODIUM CACODYLATE PH 6.5, 3.0M NACL, 30% GLYCEROL (cryoprotectant), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.82 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.53 α = 90 b = 86.44 β = 90 c = 87.09 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 CCD MARMOSAIC 300 mm CCD 2008-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-1
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 1.6 60 99.7 0.079 0.063 23.01 7.16 30243 30243
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 1.6 1.7 100 0.372 0.529 5.34 7.3 4938
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 (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 3O79 1.6 61.35 30243 28712 1531 99.71 0.15762 0.1549 0.159 0.20713 0.2056 RANDOM 20.807
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] -0.15 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_sphericity_free 22.761 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 15.526 r_sphericity_bonded 14.608 r_dihedral_angle_1_deg 6.018 r_rigid_bond_restr 6.012 r_angle_refined_deg 1.505 r_angle_other_deg 1.247 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_sphericity_free 22.761 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 15.526 r_sphericity_bonded 14.608 r_dihedral_angle_1_deg 6.018 r_rigid_bond_restr 6.012 r_angle_refined_deg 1.505 r_angle_other_deg 1.247 r_chiral_restr 0.075 r_gen_planes_refined 0.017 r_gen_planes_other 0.015 r_bond_refined_d 0.013 r_bond_other_d 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1699 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling