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Crystal structure of nitrophorin 2 complexed with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEE pdb entry 1PEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 89% saturated sodium citrate, 100 mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.377 α = 90 b = 34.377 β = 90 c = 257.256 γ = 90
Symmetry Space Group P 41 21 2
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 MAR CCD 165 mm bent Si-mirror 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 1.2 22 84.4 0.05 24 5.4 42640 42640 21.5
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 1.24 85 0.31 3.2 2.6 3225
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 FOURIER SYNTHESIS THROUGHOUT pdb entry 1PEE 1.2 22 40513 40513 2127 84.48 0.18715 0.18563 0.1787 0.21625 0.2086 RANDOM 17.842
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 10.883 r_sphericity_free 9.757 r_dihedral_angle_4_deg 8.001 r_sphericity_bonded 6.46 r_scangle_it 5.194 r_scbond_it 3.86 r_mcangle_it 3.123 r_rigid_bond_restr 2.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 10.883 r_sphericity_free 9.757 r_dihedral_angle_4_deg 8.001 r_sphericity_bonded 6.46 r_scangle_it 5.194 r_scbond_it 3.86 r_mcangle_it 3.123 r_rigid_bond_restr 2.355 r_mcbond_it 2.286 r_angle_refined_deg 2.057 r_nbtor_refined 0.307 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.214 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.143 r_bond_refined_d 0.021 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1453 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection CrystalClear data reduction CrystalClear data scaling