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High resolution structure of the apo form of the orange protein (ORP) from Desulfovibrio gigas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O13 PDB ENTRY 1O13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.1 M NA ACETATE, 0.2 M NAH2PO4 PH 4.5, 15-30% PEG 3K OR PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.08 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.078 α = 90 b = 43.078 β = 90 c = 106.085 γ = 120
Symmetry Space Group P 31 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2 106 90.7 0.05 33.7 9.9 7446 2 22
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 2 2.05 62.2 0.09 16.9 6
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 1O13 2 106 7108 347 90.51 0.18585 0.18278 0.1828 0.24448 0.2466 RANDOM 22.522
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 0.06 0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 21.366 r_dihedral_angle_3_deg 18.695 r_dihedral_angle_1_deg 8.252 r_scangle_it 4.561 r_scbond_it 2.656 r_angle_refined_deg 1.65 r_mcangle_it 1.551 r_mcbond_it 0.803 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 21.366 r_dihedral_angle_3_deg 18.695 r_dihedral_angle_1_deg 8.252 r_scangle_it 4.561 r_scbond_it 2.656 r_angle_refined_deg 1.65 r_mcangle_it 1.551 r_mcbond_it 0.803 r_chiral_restr 0.14 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 850 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling BALBES phasing