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Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome RpBphP3 from R. palustris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTU modified PDB entry 1ZTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 protein concentration of 12mg/ml in 100 mM tri-sodium citrate pH 5.6, 6% isopropanol (v/v), and 7% PEG 4000 (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.39 63.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.866 α = 90 b = 151.866 β = 90 c = 75.996 γ = 120
Symmetry Space Group P 3 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 CCD ADSC QUANTUM 315 2006-02-22 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-02-09 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97 APS 19-ID
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 2.1 50 99.3 0.077 10.7 13.9 59009 58049
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.1 2.18 100 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 modified PDB entry 1ZTU 2.2 49.75 51388 43956 3595 93.29 0.19157 0.18828 0.1913 0.23102 0.2318 RANDOM 47.92
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] 2.38 1.19 2.38 -3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.836 r_dihedral_angle_4_deg 18.399 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_1_deg 6.508 r_scangle_it 2.671 r_scbond_it 1.965 r_angle_refined_deg 1.579 r_mcangle_it 1.235 r_mcbond_it 1.075 r_angle_other_deg 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.836 r_dihedral_angle_4_deg 18.399 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_1_deg 6.508 r_scangle_it 2.671 r_scbond_it 1.965 r_angle_refined_deg 1.579 r_mcangle_it 1.235 r_mcbond_it 1.075 r_angle_other_deg 0.982 r_symmetry_vdw_refined 0.461 r_symmetry_vdw_other 0.425 r_nbd_refined 0.21 r_nbd_other 0.202 r_mcbond_other 0.186 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.096 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4731 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 86
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction 14BMC data collection HKL-2000 data reduction