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Crystal structure of nitrophorin 2 ferrous aqua complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.65 24.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.405 α = 90 b = 34.405 β = 90 c = 255.181 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 ADSC QUANTUM 315 bent Si-mirror 2004-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
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 1.6 23 97 0.05 21 4.8 21168 21168 28.7
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) 1.6 1.66 97 0.23 2.6 3.8 2039
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1PEE 1.6 23 19970 19970 1084 97.27 0.18449 0.18449 0.18212 0.22927 0.2467 RANDOM 19.075
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 -0.2 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.081 r_dihedral_angle_3_deg 13.016 r_dihedral_angle_1_deg 7.134 r_scangle_it 3.988 r_dihedral_angle_4_deg 3.196 r_scbond_it 3.085 r_mcangle_it 2.025 r_angle_refined_deg 1.893 r_mcbond_it 1.75 r_angle_other_deg 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.081 r_dihedral_angle_3_deg 13.016 r_dihedral_angle_1_deg 7.134 r_scangle_it 3.988 r_dihedral_angle_4_deg 3.196 r_scbond_it 3.085 r_mcangle_it 2.025 r_angle_refined_deg 1.893 r_mcbond_it 1.75 r_angle_other_deg 0.923 r_mcbond_other 0.361 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.227 r_symmetry_vdw_other 0.197 r_symmetry_hbond_refined 0.197 r_nbd_other 0.182 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.125 r_nbtor_other 0.086 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1434 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling