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Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% PEG 3350, 0.2 M MgSO4, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.238 α = 90 b = 111.238 β = 90 c = 115.526 γ = 120
Symmetry Space Group P 31 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 2005-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.0 NSLS X26C
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 2.5 50 100 0.136 9 29063 -2 46.2
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) 2.5 2.59 100 0.56 2 2884
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 1RTY 2.5 30 28765 1428 99 0.2 0.197 0.1929 0.251 0.2454 RANDOM 34.397
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.842 r_dihedral_angle_4_deg 23.445 r_dihedral_angle_3_deg 18.251 r_dihedral_angle_1_deg 6.068 r_scangle_it 2.88 r_scbond_it 1.849 r_angle_refined_deg 1.484 r_mcangle_it 1.342 r_mcbond_it 0.786 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.842 r_dihedral_angle_4_deg 23.445 r_dihedral_angle_3_deg 18.251 r_dihedral_angle_1_deg 6.068 r_scangle_it 2.88 r_scbond_it 1.849 r_angle_refined_deg 1.484 r_mcangle_it 1.342 r_mcbond_it 0.786 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.162 r_metal_ion_refined 0.102 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3990 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 82
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction