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X-Ray Structure of Human Phosphomannomutase 2 (PMM2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K 2 VAPOR DIFFUSION, HANGING DROP 8.5 277 10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 51.9 2.6 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.622 α = 90 b = 70.622 β = 90 c = 100.15 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 225 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-07-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-06-13 M MAD 3 1 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97243 APS 22-BM 2 SYNCHROTRON APS BEAMLINE 22-ID 0.97625, 0.97947 APS 22-ID
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 2.09 50 99 0.069 20.356 12.3 17547
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) 1,2 2.09 2.16 91.5 91.5 0.599 3.031 7
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 (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 MAD THROUGHOUT 2.09 38.745 17514 924 99.49 0.202 0.20226 0.199 0.2054 0.272 0.2619 RANDOM 56.423
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] 0.79 0.39 0.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.427 r_dihedral_angle_3_deg 17.162 r_dihedral_angle_4_deg 15.44 r_dihedral_angle_1_deg 6.85 r_scangle_it 6.65 r_scbond_it 5.216 r_mcangle_it 3.005 r_mcbond_it 1.838 r_angle_refined_deg 1.821 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.427 r_dihedral_angle_3_deg 17.162 r_dihedral_angle_4_deg 15.44 r_dihedral_angle_1_deg 6.85 r_scangle_it 6.65 r_scbond_it 5.216 r_mcangle_it 3.005 r_mcbond_it 1.838 r_angle_refined_deg 1.821 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.203 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SOLOMON phasing ARP/wARP model building