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Structure of reduced Arabidopsis thaliana cytochrome 6A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CTJ PDB ENTRY 1CTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 2.0 M AMMONIUM PHOSPHATE, 0.1 M TRIS HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.975 α = 90 b = 57.975 β = 90 c = 65.005 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.4 50.19 93.8 0.06 24 5.5 23823 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 1.39 1.44 86 0.4 3 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1CTJ 1.4 50.19 22603 1220 93.7 0.169 0.168 0.1773 0.184 0.1929 RANDOM 14.99
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] 0.43 0.21 0.43 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.034 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 10.432 r_scangle_it 2.976 r_scbond_it 2.252 r_mcangle_it 1.635 r_mcbond_it 1.401 r_angle_refined_deg 1.344 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.034 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 10.432 r_scangle_it 2.976 r_scbond_it 2.252 r_mcangle_it 1.635 r_mcbond_it 1.401 r_angle_refined_deg 1.344 r_angle_other_deg 0.889 r_nbd_refined 0.301 r_symmetry_vdw_other 0.195 r_symmetry_vdw_refined 0.185 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.172 r_symmetry_hbond_refined 0.09 r_nbtor_other 0.08 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 772 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing