1VJR

Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	273	2M sodium chloride, 0.1M MES pH 6.5, 0.1M sodium dihydrogen phosphate, 0.1M potassium dihydrogen phosphate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
5.35	76.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.998	α = 90
b = 93.998	β = 90
c = 160.365	γ = 90

Symmetry
Space Group	P 41 21 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		2003-05-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9797, 0.9999, 0.9799	ALS	8.2.2

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	2.4	94	100	0.072	14.5	4.6		28916			57.98

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	2.4	2.46	100		0.537	2.3	4.8	2087

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.4	51.17	27354	1485	99.92	0.1653	0.16381	0.19427	RANDOM	44.646

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]
1.56			1.56		-3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.945
r_dihedral_angle_3_deg	14.025
r_dihedral_angle_4_deg	13.771
r_scangle_it	8.85
r_scbond_it	6.486
r_dihedral_angle_1_deg	5.828
r_mcangle_it	3.092
r_mcbond_it	2.08
r_angle_refined_deg	1.427
r_nbd_refined	0.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.945
r_dihedral_angle_3_deg	14.025
r_dihedral_angle_4_deg	13.771
r_scangle_it	8.85
r_scbond_it	6.486
r_dihedral_angle_1_deg	5.828
r_mcangle_it	3.092
r_mcbond_it	2.08
r_angle_refined_deg	1.427
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.145
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.093
r_symmetry_hbond_refined	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2030
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.