5DEB | pdb_00005deb

2009 H1N1 PA endonuclease mutant E119D in complex with rUMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CZN	PDB entry 5CZN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1 M HEPES, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride, 200 mM rUMP

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.057	α = 90
b = 90.057	β = 90
c = 134.337	γ = 90

Symmetry
Space Group	I 4 2 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	MARMOSAIC 300 mm CCD		2014-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00522	APS	22-ID

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	2.07	50	99.7	0.066	36.82	11.9		17236

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.14	99			10.2

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 5CZN	2.14	46.21	14764	835	99.74	0.2083	0.206	0.2146	0.2487	0.2622	RANDOM	68.585

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]
0.97			0.97		-1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.975
r_dihedral_angle_4_deg	16.453
r_dihedral_angle_3_deg	15.418
r_dihedral_angle_1_deg	6.734
r_mcangle_it	3.267
r_mcbond_other	2.069
r_mcbond_it	2.068
r_angle_refined_deg	1.741
r_angle_other_deg	1.045
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1428
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing