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Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.3 277 0.2M CaAcetate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.814 α = 94.68 b = 50.08 β = 115.29 c = 52.014 γ = 116.46
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 flat mirror 2004-07-05 M SINGLE WAVELENGTH 2 1 x-ray M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979508,0.885567 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 1.3 26.45 89.3 0.036 17.5 3.2 75749 19.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.37 61.5 0.339 3.2 2 7630
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 1.3 26.45 71946 3802 89.27 0.13572 0.13402 0.1467 0.16785 0.1766 RANDOM 14.06
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] -0.24 0.37 -0.09 -0.14 0.28 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.927 r_dihedral_angle_4_deg 12.108 r_dihedral_angle_3_deg 11.94 r_sphericity_free 6.506 r_dihedral_angle_1_deg 6.461 r_scangle_it 5.375 r_scbond_it 4.135 r_sphericity_bonded 3.452 r_mcangle_it 3.171 r_mcbond_it 2.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.927 r_dihedral_angle_4_deg 12.108 r_dihedral_angle_3_deg 11.94 r_sphericity_free 6.506 r_dihedral_angle_1_deg 6.461 r_scangle_it 5.375 r_scbond_it 4.135 r_sphericity_bonded 3.452 r_mcangle_it 3.171 r_mcbond_it 2.427 r_rigid_bond_restr 1.938 r_angle_refined_deg 1.495 r_mcbond_other 1.411 r_angle_other_deg 1.052 r_symmetry_vdw_refined 0.378 r_symmetry_vdw_other 0.263 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.201 r_nbd_other 0.192 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.15 r_metal_ion_refined 0.107 r_chiral_restr 0.089 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2475 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHARP phasing REFMAC refinement CCP4 data scaling