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Crystal structure of a protein of unknown function (DUF1244) from Alcanivorax borkumensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O35 PDB entry 2O35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2M CaCl2, 20% PEG 3350. 25% Ethylene glycol added as a cryoprotectant, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.501 α = 90 b = 69.536 β = 90 c = 81.921 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ osmic mirrors 2008-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 1.8 32.19 99.6 0.058 29.526 6.8 22170 22091 -3 22.4
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 1.8 1.86 95.5 0.392 5.3 5.2 2110
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 PDB entry 2O35 1.8 32.19 22042 20910 1132 99.64 0.1888 0.1871 0.1864 0.22147 0.2217 RANDOM 17.428
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.198 r_dihedral_angle_3_deg 12.383 r_dihedral_angle_4_deg 9.958 r_dihedral_angle_1_deg 4.766 r_scangle_it 3.608 r_scbond_it 2.803 r_angle_refined_deg 1.374 r_mcangle_it 1.353 r_mcbond_it 1.019 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.198 r_dihedral_angle_3_deg 12.383 r_dihedral_angle_4_deg 9.958 r_dihedral_angle_1_deg 4.766 r_scangle_it 3.608 r_scbond_it 2.803 r_angle_refined_deg 1.374 r_mcangle_it 1.353 r_mcbond_it 1.019 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 1489 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 23
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling