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Crystal structure of red chlorophyll catabolite reductase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZXK PDB ENTRY 2ZXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 25% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.286 α = 90 b = 68.14 β = 95.32 c = 83.273 γ = 90
Symmetry Space Group P 1 21 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 QUANTUM 315 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.4 50 99.4 0.068 7.2 3.6 22833
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) 2.4 2.49 99.7 0.293 2.2 3.7 3315
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 2ZXK 2.4 20 22989 22446 1170 99.41 0.2206 0.22067 0.21635 0.2442 0.29817 0.2501 RANDOM 31.67
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] 5.28 -2.42 -2.78 -2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 20.969 r_dihedral_angle_3_deg 19.932 r_dihedral_angle_1_deg 6.775 r_scangle_it 2.221 r_angle_refined_deg 1.49 r_scbond_it 1.375 r_mcangle_it 0.918 r_mcbond_it 0.498 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 20.969 r_dihedral_angle_3_deg 19.932 r_dihedral_angle_1_deg 6.775 r_scangle_it 2.221 r_angle_refined_deg 1.49 r_scbond_it 1.375 r_mcangle_it 0.918 r_mcbond_it 0.498 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.105 r_metal_ion_refined 0.064 r_bond_refined_d 0.011 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 4352 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling MOLREP phasing