1P4T | pdb_00001p4t

Crystal structure of Neisserial surface protein A (NspA)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	277	0.06% n-decylpentaoxyethylene (c10e5), 12% (w/v) PEG 3000, 0.1 M lithium sulfate, 0.1 M N-(2-acetamido)iminodiacetic acid (ADA), 2% (v/v) isopropanol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.73	73.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.372	α = 90
b = 97.372	β = 90
c = 171.939	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 4	TOROIDAL MIRROR	2002-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.933	ESRF	ID14-1

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	2.55	40	98.6	0.07	0.07	19	12.1	10503	10350	-3.7	-3.7	69.8

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	2.55	2.64	99.7		0.375	0.375	5.2	8.7	1029

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.55	30.15	10340	10340	501	100	0.22664	0.22514	0.22	0.25791	0.26	RANDOM	39.103

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]
-0.4	-0.2		-0.4		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.318
r_scangle_it	3.33
r_scbond_it	2.018
r_angle_refined_deg	1.739
r_mcangle_it	1.351
r_angle_other_deg	0.796
r_mcbond_it	0.684
r_nbd_other	0.244
r_nbd_refined	0.2
r_symmetry_vdw_other	0.184
r_xyhbond_nbd_refined	0.161
r_symmetry_vdw_refined	0.123
r_chiral_restr	0.099
r_symmetry_hbond_refined	0.094
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1161
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	92

Software

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