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Crystal Structure of Orf6 protein from Photobacterium profundum, Mg2+-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.98 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.292 α = 90 b = 54.362 β = 90 c = 88.363 γ = 90
Symmetry Space Group I 2 2 2
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 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 46.3 96.3 24736 23821
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 1.4 1.45 76.8
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 3R87 1.4 46.3 22606 22606 1215 96.3 0.15052 0.1482 0.1533 0.19606 0.1955 RANDOM 17.875
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] -1.49 -0.87 2.36
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.03 r_dihedral_angle_2_deg 32.227 r_sphericity_bonded 19.171 r_dihedral_angle_4_deg 14.692 r_dihedral_angle_3_deg 12.263 r_dihedral_angle_1_deg 6.499 r_rigid_bond_restr 2.951 r_angle_refined_deg 1.608 r_angle_other_deg 0.903 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.03 r_dihedral_angle_2_deg 32.227 r_sphericity_bonded 19.171 r_dihedral_angle_4_deg 14.692 r_dihedral_angle_3_deg 12.263 r_dihedral_angle_1_deg 6.499 r_rigid_bond_restr 2.951 r_angle_refined_deg 1.608 r_angle_other_deg 0.903 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1055 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling