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Crystal structure of IspD from Mycobacterium smegmatis in complex with CMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 40 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CMP, 10 MM MGCL2 AND 10 MM ERYTHRITOL) AND 300 NANOLITERS SCREENING/RESERVOIR SOLUTION (10% (W/V) PEG 20,000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.03M NAF, 0.03M NAI, 0.03M NABR, AND 0.1M MOPS/NA-HEPES, PH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.59 α = 90 b = 71.7 β = 90 c = 111.89 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 110 CCD ADSC QUANTUM 4r 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.8 28 99.9 0.09 16.2 7 34794
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 1.8 1.9 99.9 0.56 3.5 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 (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 1.8 60.37 32984 1750 99.88 0.18185 0.18007 0.1806 0.21529 0.2143 RANDOM 23.465
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] 1.03 -0.86 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.107 r_dihedral_angle_4_deg 16.821 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 5.365 r_angle_refined_deg 1.254 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.107 r_dihedral_angle_4_deg 16.821 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 5.365 r_angle_refined_deg 1.254 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3156 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing