4Q04 | pdb_00004q04

Crystal structure of URE3-BP from Entomaeba histolytica without calcium

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	EnhiA.01648.a.D11.PD00049 at 11.96 mg/mL against Precipitant Synergy block 2, 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5, crystal tracking ID 248792c5, unique puck ID cjw8-9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.42	α = 90
b = 69.42	β = 90
c = 187.36	γ = 90

Symmetry
Space Group	P 43 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	RIGAKU SATURN 944+	VariMax	2013-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.9	50	91.3	0.059	20.19	5.9	37199	33977		-3	25.002

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	1.9	1.95	89.6		0.239	3.18

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 (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 3SJS	1.9	50	33961	1720	91.52	0.1849	0.182	0.19	0.2395	0.24	RANDOM	19.677

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]
-0.47			-0.47		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.022
r_dihedral_angle_4_deg	21.251
r_dihedral_angle_3_deg	13.898
r_dihedral_angle_1_deg	5.53
r_mcangle_it	1.68
r_angle_refined_deg	1.649
r_mcbond_it	1.075
r_mcbond_other	1.075
r_angle_other_deg	0.869
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3449
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	14

Software

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