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E13K 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 24% 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 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.99 α = 90 b = 60.865 β = 90 c = 71.938 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 2010-02-05 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 99.5 0.061 13.9 31814
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 1.6 1.69 0.224 13.4
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 30154 1605 99.5 0.17896 0.17747 0.1764 0.20712 0.2074 RANDOM 21.456
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] -1.13 2.6 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_dihedral_angle_4_deg 16.208 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.327 r_scangle_it 3.182 r_scbond_it 1.903 r_mcangle_it 1.126 r_angle_refined_deg 1.118 r_mcbond_it 0.593 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_dihedral_angle_4_deg 16.208 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.327 r_scangle_it 3.182 r_scbond_it 1.903 r_mcangle_it 1.126 r_angle_refined_deg 1.118 r_mcbond_it 0.593 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1852 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling