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Crystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DT1 PDB ENTRY 1DT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.44 298 0.2M Imidazole-Malate, 42% MPEG 5K, pH 5.44, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.98 α = 90 b = 86.98 β = 90 c = 31.82 γ = 120
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 2011-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.97 25.68 98.6 0.088 9.7 4.8 9951 9814 2 2
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 1.97 2.04 98.4 0.312 3.6 4.8 956
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DT1 1.97 20 9800 9333 467 98.58 0.21406 0.21315 0.2114 0.23243 0.2302 RANDOM 22.245
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.328 r_dihedral_angle_4_deg 23.904 r_dihedral_angle_3_deg 16.399 r_dihedral_angle_1_deg 5.545 r_scangle_it 3.39 r_scbond_it 2.11 r_mcangle_it 1.292 r_angle_refined_deg 1.275 r_mcbond_it 0.688 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.328 r_dihedral_angle_4_deg 23.904 r_dihedral_angle_3_deg 16.399 r_dihedral_angle_1_deg 5.545 r_scangle_it 3.39 r_scbond_it 2.11 r_mcangle_it 1.292 r_angle_refined_deg 1.275 r_mcbond_it 0.688 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 984 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 43
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling