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Structure of the chromophore binding domain of bacterial phytochrome
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.95 298 PEG 400, sodium acetate, pH 4.95, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.244 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.876 α = 90 b = 133.666 β = 90 c = 49.938 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 CCD MARRESEARCH 2004-10-25 M MAD 2 1 x-ray 98 CCD MARRESEARCH 2004-10-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.9793, 0.9791 APS 32-ID 2 SYNCHROTRON APS BEAMLINE 32-ID 0.9793, 0.9791 APS 32-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 2.5 30 97 0.056 14.2 6.7 15209
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) 2.5 2.59 90.4 0.111 10.8 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.5 20 15154 14403 751 97.08 0.23887 0.23746 0.2868 0.26569 0.3138 RANDOM 48.759
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] -7.09 -8.42 15.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_3_deg 19.545 r_dihedral_angle_4_deg 17.551 r_dihedral_angle_1_deg 6.608 r_scangle_it 1.944 r_angle_refined_deg 1.817 r_scbond_it 1.153 r_mcangle_it 0.767 r_mcbond_it 0.429 r_symmetry_vdw_refined 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_3_deg 19.545 r_dihedral_angle_4_deg 17.551 r_dihedral_angle_1_deg 6.608 r_scangle_it 1.944 r_angle_refined_deg 1.817 r_scbond_it 1.153 r_mcangle_it 0.767 r_mcbond_it 0.429 r_symmetry_vdw_refined 0.376 r_nbtor_refined 0.301 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.103 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2408 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction