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Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase (BchL) with MgADP bound: a homologue of the nitrogenase Fe protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NIP PDB ENTRY 2NIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 CAPILLARY BATCH DIFFUSION 7.8 301 20-25% PEG 3350, 200mM Magnesium formate, 10mM MgADP, pH 7.8, CAPILLARY BATCH DIFFUSION, temperature 301K
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.729 α = 90 b = 86.622 β = 90 c = 117.169 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98000 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.63 50 96.4 0.037 40 2 133747 133747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.67 93.83 0.242 4.6 2 13313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 2NIP 1.63 33.02 1.63 66727 3544 96.24 0.17529 0.17403 0.1801 0.1986 0.2053 RANDOM 14.577
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] -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.46 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 11.914 r_dihedral_angle_1_deg 6.144 r_scangle_it 6.086 r_scbond_it 4.595 r_mcangle_it 1.758 r_mcbond_it 1.434 r_angle_refined_deg 1.206 r_angle_other_deg 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.46 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 11.914 r_dihedral_angle_1_deg 6.144 r_scangle_it 6.086 r_scbond_it 4.595 r_mcangle_it 1.758 r_mcbond_it 1.434 r_angle_refined_deg 1.206 r_angle_other_deg 0.874 r_mcbond_other 0.512 r_symmetry_vdw_other 0.282 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.217 r_nbd_other 0.19 r_nbtor_refined 0.176 r_chiral_restr 0.152 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.082 r_metal_ion_refined 0.026 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4112 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling