4IXX

Crystal structure of S213G variant DAH7PS without Tyr bound from Neisseria meningitidis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HSO	PDB ENTRY 4HSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 mme, 0.4 mM MnSO4. The drop sizes were 2 uL, and the volume of the reservoir solution was 500 uL, temperature 293.15K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.064	α = 90
b = 132.432	β = 95.72
c = 75.028	γ = 90

Symmetry
Space Group	P 1 21 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 210r		2011-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

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	1.931	74.654	99.4	0.067	15.3	3.8	55141	55141

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	2.4	2.47	99.9		0.486	2.7	3.8	4518

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4HSO	2.4	19.59	55115	3384	99.25	0.1935	0.1914	0.2247	RANDOM	48.9273

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]
-1.57		-0.05	2.18		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.116
r_dihedral_angle_4_deg	17.425
r_dihedral_angle_3_deg	15.357
r_dihedral_angle_1_deg	4.962
r_mcangle_it	2.248
r_angle_refined_deg	1.444
r_mcbond_it	1.397
r_mcbond_other	1.395
r_angle_other_deg	1.24
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.116
r_dihedral_angle_4_deg	17.425
r_dihedral_angle_3_deg	15.357
r_dihedral_angle_1_deg	4.962
r_mcangle_it	2.248
r_angle_refined_deg	1.444
r_mcbond_it	1.397
r_mcbond_other	1.395
r_angle_other_deg	1.24
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10404
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	39

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.