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Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 10 MG/ML PIMA, 1 mM GDP, 10-18% PEG 8000, 200 mM CALCIUM ACETATE, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.176 α = 90 b = 72.425 β = 90 c = 138.23 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 4 2004-06-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH 2005-07-31 M MAD 3 1 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934000 ESRF ID14-1 2 SYNCHROTRON SLS BEAMLINE X06SA 0.979106, 0.979261, 0.97181 SLS X06SA
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 1,2 2.4 37.165 99.7 0.058 0.058 9 3.4 15229 15229 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.4 2.53 100 100 0.313 0.313 2.4 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.4 29.827 15202 15202 1090 99.47 0.196 0.196 0.191 0.189 0.259 0.2598 RANDOM 36.819
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] 1.21 -0.94 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 6.694 r_scangle_it 3.426 r_scbond_it 2.263 r_angle_refined_deg 1.857 r_mcangle_it 1.279 r_mcbond_it 0.863 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 6.694 r_scangle_it 3.426 r_scbond_it 2.263 r_angle_refined_deg 1.857 r_mcangle_it 1.279 r_mcbond_it 0.863 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.123 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2656 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling AMoRE phasing SHARP phasing SOLOMON phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling