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Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WSR pdb entry 1wsr, modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 PROPLEX SCREEN, H4: 1.4M NA MALONATE, BAHEA.00657.A AT 44.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.21 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.98 α = 90 b = 72.67 β = 90 c = 138.02 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 315 2009-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.6 69.01 95.3 0.044 0.044 16.45 3.5 70368 70368 -3 26.43
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) 1.6 1.64 98.9 0.493 2.6 3.6
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 MR, MR THROUGHOUT pdb entry 1wsr, modified with ccp4 program chainsaw 1.6 69.01 70311 70311 3550 95.3 0.176 0.175 0.1874 0.205 0.2158 RANDOM 17.91
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] 0.85 -0.2 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.965 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 12.325 r_dihedral_angle_1_deg 6.221 r_scangle_it 5.436 r_scbond_it 3.228 r_mcangle_it 2.136 r_angle_refined_deg 1.845 r_mcbond_it 1.236 r_angle_other_deg 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.965 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 12.325 r_dihedral_angle_1_deg 6.221 r_scangle_it 5.436 r_scbond_it 3.228 r_mcangle_it 2.136 r_angle_refined_deg 1.845 r_mcbond_it 1.236 r_angle_other_deg 1.02 r_mcbond_other 0.396 r_chiral_restr 0.12 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2823 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 1
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling