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F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3000, PEG400, glycerol, HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.389 α = 90 b = 86.089 β = 90 c = 136.775 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 PIXEL DECTRIS PILATUS 6M-F 2016-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9726 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.8 72.87 98.6 0.112 0.994 7.9 4.5 89383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 90.2 0.991 0.247 0.9 2.8 4183
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JAX 1.8 72.86 84848 4458 98.45 0.16703 0.16458 0.21364 0.2105 RANDOM 28.193
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] -0.16 1.4 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.808 r_dihedral_angle_4_deg 16.549 r_dihedral_angle_3_deg 14.237 r_long_range_B_refined 7.471 r_long_range_B_other 7.471 r_dihedral_angle_1_deg 6.61 r_scangle_other 5.951 r_scbond_it 3.923 r_scbond_other 3.92 r_mcangle_other 3.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.808 r_dihedral_angle_4_deg 16.549 r_dihedral_angle_3_deg 14.237 r_long_range_B_refined 7.471 r_long_range_B_other 7.471 r_dihedral_angle_1_deg 6.61 r_scangle_other 5.951 r_scbond_it 3.923 r_scbond_other 3.92 r_mcangle_other 3.253 r_mcangle_it 3.251 r_mcbond_it 2.358 r_mcbond_other 2.351 r_angle_refined_deg 2.016 r_angle_other_deg 1.099 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6573 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing