2FFB | pdb_00002ffb

The crystal structure of the HlyB-NBD E631Q mutant in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MT0	pdb entry 1MT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	100 mM Tris, 16% PEG 6000, 5% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.568	α = 90
b = 34.748	β = 97.97
c = 37.518	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	MARRESEARCH		2003-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	20	94.1	0.049				16370	2.3

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	1.95	94.1		0.277	2.3		16370

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1MT0	1.9	20	2.3	16370	876	94.1	0.20403	0.20161	0.21	0.25023	0.26	RANDOM	37.036

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]
-1.79		-3.29	-1.01		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.484
r_scangle_it	5.377
r_scbond_it	3.214
r_mcangle_it	2.95
r_mcbond_it	1.633
r_angle_refined_deg	1.414
r_angle_other_deg	0.837
r_symmetry_vdw_other	0.249
r_nbd_other	0.241
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.084
r_chiral_restr	0.081
r_bond_other_d	0.014
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1912
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing