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Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GDV PDB ENTRY 1GDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEGMME550, MES, ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.443 α = 82.51 b = 51.843 β = 62.08 c = 53.685 γ = 63.26
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 Si(III) 2004-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.5 50 88.3 0.04 20.9 2.9 59952 59952
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 1.5 1.55 66.9 0.183
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 THROUGHOUT PDB ENTRY 1GDV 1.5 31.47 56923 56923 3029 100 0.18767 0.18767 0.18624 0.1883 0.21451 0.2149 RANDOM 20.187
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] -0.48 0.27 0.37 0.62 -0.22 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.853 r_scangle_it 3.305 r_scbond_it 1.989 r_mcangle_it 1.385 r_angle_refined_deg 1.122 r_mcbond_it 0.706 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.853 r_scangle_it 3.305 r_scbond_it 1.989 r_mcangle_it 1.385 r_angle_refined_deg 1.122 r_mcbond_it 0.706 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3186 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing