1XZ0

Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.961	α = 90
b = 43.235	β = 91.04
c = 209.944	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 210		2003-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.116	ALS	8.3.1

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	2.8	50	94.3	0.098	14.6	3	25373	23923

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	2.8	2.9	85.5		0.444	2.2		2205

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 1ONQ	2.8	38.63	24273	22766	1157	94.29	0.21797	0.21992	0.21699	0.23	0.27712	0.28	RANDOM	52.263

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]
0.1		-0.04			-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_3_deg	18.359
r_dihedral_angle_4_deg	12.9
r_dihedral_angle_1_deg	6.364
r_scangle_it	1.923
r_angle_refined_deg	1.478
r_scbond_it	1.108
r_angle_other_deg	0.857
r_mcangle_it	0.645
r_mcbond_it	0.3
r_nbd_refined	0.191
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.18
r_nbd_other	0.178
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.148
r_symmetry_vdw_refined	0.148
r_mcbond_other	0.109
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6029
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	161

Software

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