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Crystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodopseudomonas palustris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 4000, ammonium iodide, Tris-HCl pH8.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.868 α = 90 b = 81.227 β = 90 c = 122.182 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 ADSC QUANTUM 210 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 2.4 50 98.3 0.081 8.5 3.7 27560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 88.1 0.399 2.3
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 3ab1 2.4 36.42 25218 1341 94.39 0.22053 0.21829 0.2204 0.26324 0.2661 RANDOM 49.45
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] -0.33 0.28 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.813 r_dihedral_angle_4_deg 25.637 r_dihedral_angle_3_deg 19.651 r_dihedral_angle_1_deg 7.395 r_long_range_B_refined 6.644 r_long_range_B_other 6.641 r_mcangle_it 4.551 r_mcangle_other 4.551 r_scangle_other 4.136 r_mcbond_it 2.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.813 r_dihedral_angle_4_deg 25.637 r_dihedral_angle_3_deg 19.651 r_dihedral_angle_1_deg 7.395 r_long_range_B_refined 6.644 r_long_range_B_other 6.641 r_mcangle_it 4.551 r_mcangle_other 4.551 r_scangle_other 4.136 r_mcbond_it 2.828 r_mcbond_other 2.828 r_scbond_it 2.541 r_scbond_other 2.541 r_angle_refined_deg 2.143 r_angle_other_deg 1.604 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5179 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing