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1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NP1 PDB Entry 2NP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1 M potassium cacodylate pH 5.3, 2.9 M di-ammoium hydrogen phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.006 α = 90 b = 73.987 β = 99.16 c = 65.224 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2003-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 30 99.5 0.074 8.1 3.9 40082 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.74 98.5 0.33 1 3.7
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 2NP1 1.7 30 36923 1945 96.54 0.18469 0.18469 0.18191 0.1864 0.23713 RANDOM 24.646
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] -0.2 -1.6 0.27 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.3 r_scangle_it 5.248 r_scbond_it 3.324 r_mcangle_it 2.334 r_angle_refined_deg 1.962 r_mcbond_it 1.313 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.214 r_chiral_restr 0.173 r_symmetry_vdw_refined 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.3 r_scangle_it 5.248 r_scbond_it 3.324 r_mcangle_it 2.334 r_angle_refined_deg 1.962 r_mcbond_it 1.313 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.214 r_chiral_restr 0.173 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.066 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling CNS phasing