5DMP | pdb_00005dmp

Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N9B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	285	200 mM magnesium sulfate, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.07	α = 90
b = 57.07	β = 90
c = 105.041	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	DECTRIS PILATUS 300K		2011-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.793	49.424	98.9	0.05	0.056	0.025	16.4	5	18976	18976

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.89	99.9		0.45	0.45	0.224	1.7	4.9	2759

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	3n9b	1.793	49.42	17965	974	98.59	0.1759	0.1744	0.1763	0.2045	0.2083	RANDOM	37.484

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]
0.38	0.19		0.38		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.262
r_dihedral_angle_4_deg	26.018
r_dihedral_angle_3_deg	14.832
r_dihedral_angle_1_deg	12.161
r_scbond_it	5.099
r_mcangle_it	5.053
r_mcbond_it	3.663
r_angle_refined_deg	2.07
r_chiral_restr	0.171
r_bond_refined_d	0.02
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1341
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	33

Software

Software
Software Name	Purpose
CrystalClear	data collection
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Coot	model building