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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 8 293 20% PEG3350, 0.2M AMMONIUM CLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.418 α = 90 b = 80.941 β = 100.66 c = 176.728 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 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A Photon Factory BL-5A
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 2.8 50 92 0.106 51405 -2 55.83
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 2.8 47.09 48797 2592 91.9 0.19 0.187 0.1892 0.237 0.2357 RANDOM 41.01
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] -1.62 -0.15 3.52 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_3_deg 20.625 r_dihedral_angle_4_deg 20.555 r_dihedral_angle_1_deg 6.217 r_scangle_it 2.135 r_angle_refined_deg 1.448 r_scbond_it 1.244 r_mcangle_it 0.801 r_mcbond_it 0.441 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_3_deg 20.625 r_dihedral_angle_4_deg 20.555 r_dihedral_angle_1_deg 6.217 r_scangle_it 2.135 r_angle_refined_deg 1.448 r_scbond_it 1.244 r_mcangle_it 0.801 r_mcbond_it 0.441 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.228 r_metal_ion_refined 0.148 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.099 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 12772 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 16
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling