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F218V mutant of the substrate-free form of red chlorophyll catabolite reductase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AGA PDB ENTRY 3AGA
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 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.141 α = 90 b = 84.431 β = 90 c = 132.248 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 RAYONIX MX225HE 2009-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 2.2 50 98.9 0.077 11.6 8.2 26102 26102
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 2.28 96.8 0.359 6.9 6.9 2523
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3AGA 2.2 35.58 24795 24795 1330 98.53 0.22448 0.22448 0.22087 0.2374 0.29191 0.3093 RANDOM 22.84
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] -0.45 -0.89 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 19.333 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.399 r_scbond_it 1.453 r_angle_refined_deg 1.266 r_mcangle_it 0.975 r_mcbond_it 0.508 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 19.333 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.399 r_scbond_it 1.453 r_angle_refined_deg 1.266 r_mcangle_it 0.975 r_mcbond_it 0.508 r_nbtor_refined 0.299 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.085 r_metal_ion_refined 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 4195 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling