3CJJ

Crystal structure of human rage ligand-binding domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M Na cacodylate, 0.2M Zn acetate, 11% PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.85	α = 90
b = 119.96	β = 90
c = 28.89	γ = 90

Symmetry
Space Group	P 21 21 2

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 225 mm CCD		2006-08-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.008, 1.28, 1.283	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	35.18	99.8	0.09	11.38			23066		-3	33.657

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	2	100		0.589	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.85	35	23063	1154	100	0.21	0.209	0.24	RANDOM	28.2

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]
-1.02			-1.05		2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.082
r_dihedral_angle_4_deg	24.105
r_dihedral_angle_3_deg	18.168
r_dihedral_angle_1_deg	8.127
r_scangle_it	4.466
r_scbond_it	2.695
r_angle_refined_deg	1.988
r_mcangle_it	1.876
r_mcbond_it	1.146
r_nbtor_refined	0.312
r_nbd_refined	0.239
r_symmetry_vdw_refined	0.225
r_xyhbond_nbd_refined	0.212
r_symmetry_hbond_refined	0.204
r_metal_ion_refined	0.202
r_chiral_restr	0.118
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1687
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing