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The structure of YcaO from Methanopyrus kandleri bound with AMPPCP and Mg2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 282.1 0.02 M sodium formate, 0.02
M ammonium acetate, 0.02 M sodium citrate (tribasic), 0.02 M sodium potassium tartrate, 0.02 M sodium
oxamate, 0.05 M HEPES pH=7.5, 0.05 M MOPS pH=7.5, 20% glycerol, and 10% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.53 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.193 α = 90 b = 106.755 β = 103.66 c = 141.446 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX-300 2017-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 137.5 98.1 18.1 7.6 155349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.359
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.3 25 147409 7662 98.04 0.18705 0.18498 0.22643 0.2152 RANDOM 59.885
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] -3.74 1.17 1.27 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 19.354 r_dihedral_angle_3_deg 16.955 r_long_range_B_refined 9.543 r_dihedral_angle_1_deg 5.956 r_mcangle_it 4.636 r_scbond_it 3.99 r_mcbond_it 2.925 r_angle_refined_deg 1.442 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 19.354 r_dihedral_angle_3_deg 16.955 r_long_range_B_refined 9.543 r_dihedral_angle_1_deg 5.956 r_mcangle_it 4.636 r_scbond_it 3.99 r_mcbond_it 2.925 r_angle_refined_deg 1.442 r_chiral_restr 0.094 r_bond_refined_d 0.009 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 17401 Nucleic Acid Atoms Solvent Atoms 1497 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHARP phasing