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Crystal structure of Regnase PIN domain, form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.7 M NaCl, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.96 58.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.333 α = 90 b = 113.333 β = 90 c = 78.373 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2009-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 26.94 92.9 34.3 10.4 16940
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 2.6 2.69 67.8 0.255 7.9 8.2
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 5H9V 2.6 26.94 16057 862 92.67 0.19347 0.19144 0.1996 0.23142 0.2402 RANDOM 73.875
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] -3.21 -3.21 -3.21 10.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_3_deg 19.722 r_dihedral_angle_4_deg 18.495 r_long_range_B_refined 7.402 r_long_range_B_other 7.401 r_dihedral_angle_1_deg 6.778 r_scangle_other 5.617 r_mcangle_it 4.688 r_mcangle_other 4.687 r_scbond_it 3.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_3_deg 19.722 r_dihedral_angle_4_deg 18.495 r_long_range_B_refined 7.402 r_long_range_B_other 7.401 r_dihedral_angle_1_deg 6.778 r_scangle_other 5.617 r_mcangle_it 4.688 r_mcangle_other 4.687 r_scbond_it 3.676 r_scbond_other 3.675 r_mcbond_it 3.116 r_mcbond_other 3.115 r_angle_refined_deg 1.718 r_angle_other_deg 1.155 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2658 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing