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E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLM PDB ENTRY 1FLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 22% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.129 α = 90 b = 60.443 β = 90 c = 72.002 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 95 CCD ADSC QUANTUM 270 2009-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.6 20 98.6 0.125 14 31369
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) 1.6 1.69 0.294 14.3
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 PDB ENTRY 1FLM 1.6 20 29731 1580 98.56 0.19419 0.19265 0.1909 0.22381 0.2249 RANDOM 14.442
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] -0.35 0.92 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_3_deg 11.223 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.583 r_scbond_it 1.552 r_angle_refined_deg 1.01 r_mcangle_it 0.957 r_mcbond_it 0.487 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_3_deg 11.223 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.583 r_scbond_it 1.552 r_angle_refined_deg 1.01 r_mcangle_it 0.957 r_mcbond_it 0.487 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling