6NYQ

Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound to a Fab fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2928% tacsimate pH 6.0, 16% PEG 3350, 10 mM phenol
Crystal Properties
Matthews coefficientSolvent content
2.4349.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.924α = 90
b = 55.238β = 99.35
c = 99.639γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.853099.89.93.371330
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.921000.6720.6111.973.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.853071330378399.570.165810.163720.20411RANDOM29.376
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]
-0.320.310.77-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg16.951
r_dihedral_angle_3_deg12.652
r_long_range_B_refined7.891
r_long_range_B_other7.89
r_dihedral_angle_1_deg6.839
r_scangle_other6.086
r_scbond_it4.233
r_scbond_other4.233
r_mcangle_other3.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg16.951
r_dihedral_angle_3_deg12.652
r_long_range_B_refined7.891
r_long_range_B_other7.89
r_dihedral_angle_1_deg6.839
r_scangle_other6.086
r_scbond_it4.233
r_scbond_other4.233
r_mcangle_other3.467
r_mcangle_it3.463
r_mcbond_it2.611
r_mcbond_other2.609
r_angle_refined_deg1.677
r_angle_other_deg0.858
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5576
Nucleic Acid Atoms
Solvent Atoms628
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing