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Deinococcus radiodurans BphP PAS-GAF H290T mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.95 297 67 mM Sodium acetate, 3.3 % PEG400, 1mM DTT, 30% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.81 α = 90 b = 53.03 β = 93.3 c = 135.88 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 4M 2015-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.4 47.33 99.7 0.108 0.124 0.997 7.48 4.25 132351 -3 15.679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 99.5 1.362 1.552 0.336 0.93 4.26
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 5K5B 1.4 47.33 125781 6620 99.75 0.15046 0.14795 0.1584 0.19816 0.2064 RANDOM 24.18
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] 0.13 -0.41 0.06 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.795 r_sphericity_free 32.082 r_dihedral_angle_4_deg 14.657 r_sphericity_bonded 13.416 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.958 r_long_range_B_refined 6.368 r_scangle_other 6.16 r_long_range_B_other 6.112 r_scbond_it 5.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.795 r_sphericity_free 32.082 r_dihedral_angle_4_deg 14.657 r_sphericity_bonded 13.416 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.958 r_long_range_B_refined 6.368 r_scangle_other 6.16 r_long_range_B_other 6.112 r_scbond_it 5.569 r_scbond_other 5.569 r_mcangle_it 5.401 r_mcangle_other 5.4 r_rigid_bond_restr 5.167 r_mcbond_it 4.745 r_mcbond_other 4.719 r_angle_refined_deg 2.551 r_angle_other_deg 1.219 r_chiral_restr 0.155 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4790 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 126
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement