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Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG3350, 0.2M AMMONIUM CLORIDE, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.302 α = 90 b = 80.92 β = 100.87 c = 176.235 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 2007-05-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97931, 0.97950, 0.96426, 0.98338 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 2.5 50 99.9 0.077 78168 -2 50.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.5 34.75 74193 3922 99.9 0.21 0.208 0.208 0.248 0.2458 RANDOM 36.28
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] 0.4 1.48 1.73 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_3_deg 19.599 r_dihedral_angle_4_deg 18.968 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.261 r_scbond_it 1.453 r_angle_refined_deg 1.351 r_mcangle_it 0.879 r_mcbond_it 0.626 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_3_deg 19.599 r_dihedral_angle_4_deg 18.968 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.261 r_scbond_it 1.453 r_angle_refined_deg 1.351 r_mcangle_it 0.879 r_mcbond_it 0.626 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.093 r_metal_ion_refined 0.029 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_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 307 Heterogen Atoms 16
Software Software Software Name Purpose SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling