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human glycinamide ribonucleotide Transformylase at pH 4.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MEJ PDB ENTRY 1MEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 282 1.9-2.1M Ammonium Sulfate, 100mM Na Acetate pH 4.2-4.6, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 4.5 72.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.13 α = 90 b = 78.13 β = 90 c = 230.91 γ = 120
Symmetry Space Group P 65 2 2
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 9 2001-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.976 SSRL BL11-1
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 1.72 43.92 94.8 0.072 23.4 2.4 40379 -3
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) 1.72 1.78 99 0.418 1.65 1.9 16675
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MEJ 1.72 43.85 45030 40379 4458 0.226 0.226 0.223 0.24 0.2621 RANDOM 18.691
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] 0.59 0.29 0.59 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.217 r_dihedral_angle_1_deg 3.641 r_scangle_it 3.352 r_scbond_it 1.902 r_angle_refined_deg 1.142 r_mcangle_it 1.135 r_mcbond_it 0.57 r_symmetry_hbond_refined 0.499 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.217 r_dihedral_angle_1_deg 3.641 r_scangle_it 3.352 r_scbond_it 1.902 r_angle_refined_deg 1.142 r_mcangle_it 1.135 r_mcbond_it 0.57 r_symmetry_hbond_refined 0.499 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1531 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction