1ONQ | pdb_00001onq

Crystal Structure of CD1a in Complex with a Sulfatide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GZQ	PDB ENTRY 1GZQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	277	MPEG 2000, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.407	α = 90
b = 42.711	β = 90.78
c = 204.217	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 4		2002-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2.15	50	91.6	0.067	22.5	3.8		48912

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	2.15	2.19	76.6		0.44	2.2

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 1GZQ	2.15	40	46342	46342	2236	92	0.229	0.227	0.25	0.276	0.29	RANDOM	13.91

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]
-0.06			0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.87
r_scangle_it	2.532
r_scbond_it	1.588
r_angle_refined_deg	1.495
r_mcangle_it	1.076
r_angle_other_deg	0.901
r_mcbond_it	0.578
r_symmetry_vdw_other	0.256
r_nbd_other	0.235
r_xyhbond_nbd_refined	0.227
r_symmetry_hbond_refined	0.192
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.112
r_nbtor_other	0.085
r_bond_refined_d	0.012
r_bond_other_d	0.002
r_gen_planes_refined	0.001
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6104
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	237

Software

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