3GMR | pdb_00003gmr

Structure of mouse CD1d in complex with C8Ph, different space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GML	PDB entry 3GML

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.27	α = 90
b = 107.23	β = 90
c = 109.42	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	MARMOSAIC 325 mm CCD	flat mirror	2008-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9795	SSRL	BL11-1

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	1.9	30	99.2	0.059	16.5	3.7	39777	39777		-3	28.2

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	1.9	2	99.7		0.354	3.8	3.9	5609

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 (All)	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 3GML	1.9	30	39777	37782	1995	99.17	0.18838	0.18838	0.18617	0.1943	0.22974	0.235	RANDOM	16.694

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]
-0.38			-1.11		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.649
r_dihedral_angle_4_deg	22.474
r_dihedral_angle_3_deg	14.131
r_dihedral_angle_1_deg	6.79
r_angle_refined_deg	2.048
r_bond_refined_d	0.023
r_chiral_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3010
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	222

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling