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1.96 A Crystal structure of H60C mutant of nitrophorin complexed with histamine
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, 2.9 M di-ammonium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.82 α = 90 b = 73.85 β = 98.57 c = 65.38 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 RIGAKU RAXIS IV osmic confocal mirrors 2003-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.96 27 92 0.038 11.2 2.1 26246 22695
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) 1.96 2.06 70.4 0.038 0.0125 3.4 1.08 3724
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 2NP1 1.96 27 22659 22659 1192 90.75 0.18703 0.18703 0.18498 0.1955 0.22562 RANDOM 33.658
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] -0.27 -2.7 -0.12 -0.42
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.151 r_dihedral_angle_1_deg 5.745 r_scbond_it 4.217 r_mcangle_it 2.871 r_angle_refined_deg 1.997 r_mcbond_it 1.729 r_angle_other_deg 0.991 r_symmetry_vdw_other 0.33 r_nbd_other 0.262 r_symmetry_vdw_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.151 r_dihedral_angle_1_deg 5.745 r_scbond_it 4.217 r_mcangle_it 2.871 r_angle_refined_deg 1.997 r_mcbond_it 1.729 r_angle_other_deg 0.991 r_symmetry_vdw_other 0.33 r_nbd_other 0.262 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.206 r_chiral_restr 0.163 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.092 r_bond_refined_d 0.032 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2878 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling CNS phasing