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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 2.71 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.354 α = 90 b = 80.615 β = 101.17 c = 176.22 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 210 2008-02-06 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 97.9 0.141 48730 -2 63.03
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 2.9 39.9 46241 2467 97.8 0.208 0.205 0.2077 0.257 0.2576 RANDOM 26
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] -0.8 0.89 1.64 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_3_deg 21.529 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_1_deg 6.256 r_scangle_it 2.474 r_angle_refined_deg 1.559 r_scbond_it 1.46 r_mcangle_it 0.904 r_mcbond_it 0.492 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_3_deg 21.529 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_1_deg 6.256 r_scangle_it 2.474 r_angle_refined_deg 1.559 r_scbond_it 1.46 r_mcangle_it 0.904 r_mcbond_it 0.492 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.296 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.112 r_bond_refined_d 0.013 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 12721 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 16
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling