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Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 NANODROP, 0.2M Sodium thiocyanate, 20% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.037 α = 90 b = 64.032 β = 90 c = 153.64 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 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-11-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97932, 0.91837 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 29.553 99.7 0.102 0.102 5.2 3.7 55436 19.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 100 0.643 0.643 1.2 3.7 4067
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.75 29.553 55402 2813 99.54 0.168 0.166 0.1712 0.201 0.2046 RANDOM 16.815
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] -0.12 0.74 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.638 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 12.442 r_scangle_it 6.212 r_dihedral_angle_1_deg 4.491 r_scbond_it 4.456 r_mcangle_it 2.551 r_mcbond_it 1.585 r_angle_refined_deg 1.474 r_angle_other_deg 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.638 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 12.442 r_scangle_it 6.212 r_dihedral_angle_1_deg 4.491 r_scbond_it 4.456 r_mcangle_it 2.551 r_mcbond_it 1.585 r_angle_refined_deg 1.474 r_angle_other_deg 0.98 r_mcbond_other 0.72 r_symmetry_vdw_refined 0.494 r_symmetry_vdw_other 0.351 r_nbd_refined 0.231 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.146 r_metal_ion_refined 0.117 r_chiral_restr 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_xyhbond_nbd_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3574 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing