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The crystal structure of PsbP from Zea mays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.2M tri-Ammonium Citate PH7.0, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.9 35.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.058 α = 83.41 b = 38.328 β = 66.4 c = 61.116 γ = 63.53
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 210r 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.26 Photon Factory AR-NW12A
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 50 94.8 0.03 44.3 3.9 39272 37230 1.5 1.5
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 1.63 90.5 0.131
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1V2B 1.6 32.09 1 37230 35331 1860 94.79 0.171 0.17086 0.16974 0.179 0.19294 0.2053 RANDOM 16.087
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] 0.01 -0.04 0.01 0.03 -0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.24 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 12.459 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.272 r_long_range_B_other 5.101 r_scangle_other 3.016 r_mcangle_it 2.53 r_mcangle_other 2.53 r_scbond_it 1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.24 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 12.459 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.272 r_long_range_B_other 5.101 r_scangle_other 3.016 r_mcangle_it 2.53 r_mcangle_other 2.53 r_scbond_it 1.859 r_scbond_other 1.859 r_mcbond_it 1.477 r_mcbond_other 1.473 r_angle_refined_deg 1.216 r_angle_other_deg 0.973 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2559 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling