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F218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZXL PDB ENTRY 2ZXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 35% PEG 2000 monomethyl ether, 0.1M ammonium acetate, 3% dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.089 α = 90 b = 84.321 β = 90 c = 131.518 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 RIGAKU JUPITER 210 2009-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 2 20 99.6 0.059 10.6 5.9 34491 34491
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 2 2.07 100 0.356 8 6 3425
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 2ZXL 2 20 32702 32702 1735 99.47 0.21181 0.21181 0.20885 0.2269 0.26992 0.2812 RANDOM 20.784
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] -0.08 -0.32 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.591 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 16.736 r_dihedral_angle_1_deg 5.457 r_scangle_it 1.965 r_angle_refined_deg 1.526 r_scbond_it 1.166 r_mcangle_it 0.828 r_mcbond_it 0.428 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.591 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 16.736 r_dihedral_angle_1_deg 5.457 r_scangle_it 1.965 r_angle_refined_deg 1.526 r_scbond_it 1.166 r_mcangle_it 0.828 r_mcbond_it 0.428 r_nbtor_refined 0.295 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.112 r_metal_ion_refined 0.088 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4225 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling