☰ 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 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.596 α = 90 b = 81.219 β = 100.86 c = 175.928 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 2007-06-16 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 2.3 50 99.9 0.071 100467 -2 41.6
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 2.3 34.06 95395 5015 99.8 0.193 0.191 0.1905 0.232 0.2302 RANDOM 37.31
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] 0.08 0.72 1.25 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_3_deg 18.317 r_dihedral_angle_4_deg 18 r_dihedral_angle_1_deg 5.606 r_scangle_it 1.933 r_angle_refined_deg 1.321 r_scbond_it 1.148 r_mcangle_it 0.72 r_mcbond_it 0.371 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_3_deg 18.317 r_dihedral_angle_4_deg 18 r_dihedral_angle_1_deg 5.606 r_scangle_it 1.933 r_angle_refined_deg 1.321 r_scbond_it 1.148 r_mcangle_it 0.72 r_mcbond_it 0.371 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.201 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.087 r_bond_refined_d 0.009 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 12724 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms 106
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling