2IF7 | pdb_00002if7

Crystal Structure of NTB-A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	0.4-0.5 M CaCl2, 0.1 M HEPES pH 7.4, 1.0 mM Pt(NH3)2Cl2, 4% PEG-400, Vapor diffusion, Sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.196	α = 90
b = 148.452	β = 112.86
c = 86.572	γ = 90

Symmetry
Space Group	C 1 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 315		2005-10-20	M	MAD
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9789,0.9791,0.9714	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	40	99.7	0.059	0.048	15.1	3.2	28402	28402			51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	99.9		0.348	0.303	3.08	3.2	2838

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	MAD	THROUGHOUT	3	40	28151	28151	1413	99.67	0.216	0.216	0.213	0.2081	0.266	0.2602	RANDOM	83.603

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]
2.85		3.14	-1.44		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.35
r_dihedral_angle_3_deg	19.258
r_dihedral_angle_4_deg	15.413
r_dihedral_angle_1_deg	6.209
r_scangle_it	4.239
r_scbond_it	2.517
r_mcangle_it	1.793
r_angle_refined_deg	1.085
r_mcbond_it	1.004
r_nbtor_refined	0.332
r_nbd_refined	0.299
r_symmetry_vdw_refined	0.293
r_symmetry_metal_ion_refined	0.239
r_xyhbond_nbd_refined	0.207
r_metal_ion_refined	0.164
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5960
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
Coot	model building
O	model building