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NMDA bound to compound 288
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 282.15 20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.85 α = 90 b = 71.53 β = 90 c = 96.3 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 RIGAKU SATURN 944 2015-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 23.16 92 0.071 0.995 11.2 3 21502
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.285 0.853 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 23.155 21474 1040 91.445 0.179 0.1773 0.1776 0.2145 0.2148 RANDOM 21.419
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] -0.317 0.817 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.774 r_dihedral_angle_3_deg 13.456 r_lrange_it 7.268 r_lrange_other 7.187 r_dihedral_angle_1_deg 6.933 r_dihedral_angle_2_deg 6.304 r_scangle_other 4.229 r_scangle_it 4.223 r_mcangle_other 3.314 r_mcangle_it 3.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.774 r_dihedral_angle_3_deg 13.456 r_lrange_it 7.268 r_lrange_other 7.187 r_dihedral_angle_1_deg 6.933 r_dihedral_angle_2_deg 6.304 r_scangle_other 4.229 r_scangle_it 4.223 r_mcangle_other 3.314 r_mcangle_it 3.312 r_scbond_other 2.584 r_scbond_it 2.582 r_mcbond_it 2.096 r_mcbond_other 2.096 r_angle_refined_deg 1.549 r_angle_other_deg 0.545 r_nbd_other 0.234 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.216 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2226 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing