1Z5L | pdb_00001z5l

Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CD1	PDB Entry 1CD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	PEG 4000, calcium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.451	α = 90
b = 77.045	β = 107.63
c = 111.014	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	120	CCD	ADSC QUANTUM 315		2004-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.2	50		0.075	20.8	2.4		48471

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.25	86.9		0.37	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB Entry 1CD1	2.2	39.68	44014	44014	1414	93.72	0.24321	0.24156	0.24	0.29368	0.29	RANDOM	71.352

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]
-0.01		0.02	-0.04		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.895
r_dihedral_angle_4_deg	22.531
r_dihedral_angle_3_deg	17.989
r_dihedral_angle_1_deg	5.792
r_scangle_it	2.552
r_angle_refined_deg	1.848
r_scbond_it	1.757
r_mcangle_it	1.135
r_mcbond_it	0.737
r_nbtor_refined	0.313
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.149
r_bond_refined_d	0.015
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5911
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	214

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
MOLREP	phasing