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Mouse galactocerebrosidase in complex with saposin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CCE 4CCE, 4DDJ experimental model PDB 4DDJ 4CCE, 4DDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 800 nL of protein (90 uM GALC plus 180 uM SapA) was mixed with 800 nL of reservoir solution (75 mM Sodium citrate pH 5.6, 11% PEG 3350) and equilibrated against 200 uL reservoirs at 20C.
Crystal Properties Matthews coefficient Solvent content 5.41 77.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.183 α = 90 b = 187.183 β = 90 c = 360.24 γ = 120
Symmetry Space Group P 62 2 2
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-F Toroidal mirrors 2015-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92818 Diamond I04-1
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 3.6 180.12 100 0.386 0.945 9.3 25.6 44024 61.93
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 3.6 3.7 100 2.946 0.677 25.2
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 4CCE, 4DDJ 3.6 162.11 43825 2138 99.7 0.218 0.217 0.2256 0.231 0.2308 RANDOM 101.63
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] -0.463 -0.463 0.9261
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.39 t_omega_torsion 3.38 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.39 t_omega_torsion 3.38 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11522 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 220
Software Software Software Name Purpose BUSTER refinement DIALS data reduction Aimless data scaling PHASER phasing