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Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 20% PEG3350, 0.2M SODIUM CLORIDE, 0.1M MOPS-NAOH(PH7.0), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.442 α = 102.53 b = 81.44 β = 110.89 c = 95.864 γ = 94.44
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 210 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 2.9 50 0.093 42863 -2 69.55
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 2ZMP 2.91 40.05 40688 2171 89 0.215 0.211 0.212 0.275 0.2686 RANDOM 56.64
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] 3.88 1 -0.63 -2.41 -0.87 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 21.76 r_dihedral_angle_1_deg 6.947 r_scangle_it 1.844 r_angle_refined_deg 1.484 r_scbond_it 1.072 r_mcangle_it 0.765 r_mcbond_it 0.419 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 21.76 r_dihedral_angle_1_deg 6.947 r_scangle_it 1.844 r_angle_refined_deg 1.484 r_scbond_it 1.072 r_mcangle_it 0.765 r_mcbond_it 0.419 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.101 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_refined 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 12760 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 16
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling