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Dihydrodipicolinate synthase from shewanella benthica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0S PDB ID 3G0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 281 0.2m AMMONIUM SULFATE, 25%(W/V) PEG 3350, 0.1 BIS-TRIS (PH 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 3.49 64.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.09 α = 90 b = 84.03 β = 90 c = 143.72 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 ADSC QUANTUM 315r 2010-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 2.5 72.54 99.7 3.7 31280
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 2.5 2.64 98.2 3.8
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 (All) 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 ID 3G0S 2.5 40.33 29569 29569 1572 99.28 0.20162 0.20162 0.19907 0.2018 0.25008 0.2495 RANDOM 44.296
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] 5.14 -2.21 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.136 r_dihedral_angle_4_deg 17.988 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_1_deg 6.431 r_scangle_it 3.703 r_scbond_it 2.092 r_angle_refined_deg 1.543 r_mcangle_it 1.37 r_mcbond_it 0.707 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.136 r_dihedral_angle_4_deg 17.988 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_1_deg 6.431 r_scangle_it 3.703 r_scbond_it 2.092 r_angle_refined_deg 1.543 r_mcangle_it 1.37 r_mcbond_it 0.707 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4397 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 38
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling