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Crystal structure of the SmHasA mutant H83A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B2V PDB ENTRY 1B2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 DROPS WERE PREPARED BY MIXING 2MICROL OF THE PROTEIN SOLUTION WITH 1 MICROL OF THE RESERVOIR SOLUTION THAT CONTAINED 100 MM SODIUM CACODYLATE AT PH 6.5, 200 MM ZN(OAC)2 AND 10 % (V/V) 2-PROPANOL. THE BROWNISH CRYSTALS GREW OVER A PERIOD OF 2 MONTHS AT 20 DEGREES C.
Crystal Properties Matthews coefficient Solvent content 5 75.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.67 α = 90 b = 110.67 β = 90 c = 52.355 γ = 120
Symmetry Space Group P 32 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 2002-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.6 40 99.2 0.06 10.5 4.2 18702
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 2.6 2.69 99.9 0.44 2.3 4.2
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 1B2V 2.7 40 9813 494 99.2 0.238 0.236 0.2601 0.274 0.2972 RANDOM 41.22
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] 4.25 2.12 4.25 -6.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.68 r_scangle_it 1.579 r_angle_refined_deg 1.533 r_mcangle_it 1.035 r_scbond_it 1.01 r_angle_other_deg 0.93 r_mcbond_it 0.557 r_symmetry_vdw_refined 0.28 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.68 r_scangle_it 1.579 r_angle_refined_deg 1.533 r_mcangle_it 1.035 r_scbond_it 1.01 r_angle_other_deg 0.93 r_mcbond_it 0.557 r_symmetry_vdw_refined 0.28 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.246 r_nbd_other 0.225 r_symmetry_vdw_other 0.21 r_symmetry_hbond_refined 0.127 r_nbtor_other 0.091 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 1260 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing