3OMF | pdb_00003omf

Crystal structure of a histidine triad family protein from Entamoeba histolytica, bound to AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OJ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	Internal tracking number 217183B6. JCSG screen condition B6: 40% v/v ethanol, 5% w/v PEG 1000, phosphate-citrate buffer pH 4.2, EnhiA.01296.a.A1 PS00632 at 83.2 mg/ml, 10 mM AMP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.58	α = 90
b = 60.63	β = 90
c = 67.88	γ = 90

Symmetry
Space Group	C 2 2 21

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	RIGAKU SATURN 944+		2010-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.541780

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	1.8	34.56	91.6	0.023	52.96	5.8	10570	9684		-3	16.256

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	1.8	1.85	80.3		0.045	21.4	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MR, MR	THROUGHOUT	3OJ7	1.8	34.56	10570	9660	467	91.39	0.148	0.148	0.146	0.16	0.191	0.19	RANDOM	9.817

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]
0.25			-0.21		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.727
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	12.426
r_dihedral_angle_1_deg	6.332
r_scangle_it	3.185
r_scbond_it	1.922
r_angle_refined_deg	1.516
r_mcangle_it	1.197
r_angle_other_deg	0.901
r_mcbond_it	0.639

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.727
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	12.426
r_dihedral_angle_1_deg	6.332
r_scangle_it	3.185
r_scbond_it	1.922
r_angle_refined_deg	1.516
r_mcangle_it	1.197
r_angle_other_deg	0.901
r_mcbond_it	0.639
r_mcbond_other	0.165
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	879
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.