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Mycoplasma pneumoniae CdaM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% (v/v) PEG MME 2000
0.1M Na-HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.88 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.84 α = 90 b = 80.42 β = 93.13 c = 44.444 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 100 PIXEL DECTRIS EIGER X 16M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.25 50 99.3 0.122 0.132 0.998 11.68 6.9 12934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 1.308 1.412 0.639
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 38.854 12917 669 99.247 0.201 0.1978 0.1972 0.2494 0.2466 51.813
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] -0.028 -0.017 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.262 r_dihedral_angle_6_deg 15.718 r_lrange_other 9.826 r_lrange_it 9.821 r_scangle_it 7.68 r_scangle_other 7.678 r_dihedral_angle_1_deg 5.557 r_mcangle_it 5.48 r_mcangle_other 5.478 r_scbond_it 4.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.262 r_dihedral_angle_6_deg 15.718 r_lrange_other 9.826 r_lrange_it 9.821 r_scangle_it 7.68 r_scangle_other 7.678 r_dihedral_angle_1_deg 5.557 r_mcangle_it 5.48 r_mcangle_other 5.478 r_scbond_it 4.965 r_scbond_other 4.964 r_dihedral_angle_2_deg 4.26 r_mcbond_other 3.706 r_mcbond_it 3.705 r_angle_refined_deg 1.085 r_angle_other_deg 0.377 r_symmetry_nbd_other 0.211 r_nbd_refined 0.197 r_nbd_other 0.192 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2386 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing