2NZ7 | pdb_00002nz7

Crystal Structure Analysis of Caspase-recruitment Domain (CARD) of Nod1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	20 % PEG 6000, 0.067 M MES (pH 6.0), 0.1 M diammonium hydrogen citrate, 0.09 M NaI, 0.001 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.091	α = 90
b = 79.091	β = 90
c = 80.863	γ = 120

Symmetry
Space Group	P 31 2 1

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	ADSC QUANTUM 210		2006-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.977	CHESS	F2

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	1.823	68.519		0.076	26.4	10.4	26612	26612			25.7

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)
	1.823				0.516	4.6	9.8	2617

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIR	THROUGHOUT	1.9	35.53	23436	23436	1187	100	0.222	0.222	0.22	0.24	0.266	0.28	RANDOM	27.17

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.166
r_dihedral_angle_3_deg	14.255
r_dihedral_angle_4_deg	12.78
r_sphericity_free	7.478
r_dihedral_angle_1_deg	5.873
r_scangle_it	4.533
r_sphericity_bonded	3.392
r_scbond_it	3.209
r_mcangle_it	2.531
r_rigid_bond_restr	2.414
r_mcbond_it	1.695
r_angle_refined_deg	1.672
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.285
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1554
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
HKL-2000	data scaling