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Crystal structure of cytochrome c peroxidase, N184R mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBY PDB ENTRY 1ZBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 22% 2-methyl-2,4-pentanediol (MPD), 0.05M Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.304 α = 90 b = 75.916 β = 90 c = 51.223 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2005-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.06 50 93.3 0.06 0.06 13.3 4.2 176123 -3
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) 1.06 1.08 95.9 0.64 0.64 2.5 3.3
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 1ZBY 1.06 10 163838 163838 9168 86.6 0.1705 0.1705 0.1633 0.1621 0.1992 0.1661 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 13 1594 2985
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.093 s_non_zero_chiral_vol 0.085 s_anti_bump_dis_restr 0.039 s_similar_adp_cmpnt 0.036 s_from_restr_planes 0.0293 s_angle_d 0.028 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 43
Software Software Software Name Purpose SHELXL-97 refinement SHELXD phasing CNS refinement DENZO data reduction HKL-2000 data scaling ADSC data collection