☰ Navigation Tabs
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 16% PEG4000, 0.2M SODIUM/POTASSIUM PHOSPHATE(PH5.0), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.8 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.632 α = 90 b = 81.278 β = 100.43 c = 177.103 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 2007-10-14 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 2.9 50 92 0.106 46513 -2 73.23
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 47.25 42703 2167 88.2 0.238 0.235 0.2364 0.298 0.2957 RANDOM 49.91
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] -0.24 1.08 1.79 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_3_deg 20.83 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_1_deg 5.699 r_scangle_it 1.655 r_angle_refined_deg 1.347 r_scbond_it 0.952 r_mcangle_it 0.647 r_mcbond_it 0.354 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_3_deg 20.83 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_1_deg 5.699 r_scangle_it 1.655 r_angle_refined_deg 1.347 r_scbond_it 0.952 r_mcangle_it 0.647 r_mcbond_it 0.354 r_nbtor_refined 0.308 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.099 r_chiral_restr 0.084 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.01 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 12740 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 106
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling