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Crystal structure of Neanderthal glycine decarboxylase (P-protein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.873 α = 90 b = 124.381 β = 98.57 c = 201.304 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 PILATUS 6M 2017-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.98 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 47.9 99.9 0.192 0.993 5.3 5.1 245944 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.64 1.2 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6I33 2.1 47.9 233556 12259 99.8 0.218 0.216 0.2229 0.243 0.2469 RANDOM 36.11
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] -1.86 1.66 0.85 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.464 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 6.12 r_long_range_B_other 6.113 r_scangle_other 3.817 r_scbond_it 2.551 r_scbond_other 2.551 r_mcangle_it 2.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.464 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 6.12 r_long_range_B_other 6.113 r_scangle_other 3.817 r_scbond_it 2.551 r_scbond_other 2.551 r_mcangle_it 2.406 r_mcangle_other 2.406 r_angle_refined_deg 1.915 r_angle_other_deg 1.619 r_mcbond_it 1.609 r_mcbond_other 1.608 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29751 Nucleic Acid Atoms Solvent Atoms 1359 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing