3TFJ | pdb_00003tfj

DMSP-dependent demethylase from P. ubique - with cofactor THF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WOO	PDB entries 1WOO, 1V5V
experimental model	PDB	1V5V	PDB entries 1WOO, 1V5V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	6.8	298	25 mM HEPES, 325 mM NaCl, 20% PEG. PEG increased to 30% for cryo. Soaked with THF under anaerobic conditions. , pH 6.8, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.746	α = 90
b = 121.665	β = 100.3
c = 59.336	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD	vertical focusing mirrors	2008-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.98	APS	22-ID

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	1.6	50	99	0.117	17.4	12.6	98269	97287			22.9

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	1.6	1.66	94.9		0.232	5	6.7	9824

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 (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 entries 1WOO, 1V5V	1.6	36.11	98575	94862	2389	98.65	0.12762	0.12641	0.1382	0.17645	0.1855	RANDOM	22.905

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]
0.63		1.42	-0.03		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.939
r_dihedral_angle_4_deg	20.161
r_dihedral_angle_3_deg	15.398
r_dihedral_angle_1_deg	7.559
r_scangle_it	6.777
r_scbond_it	4.818
r_mcangle_it	3.312
r_mcbond_it	2.235
r_rigid_bond_restr	2.062
r_angle_refined_deg	1.949
r_angle_other_deg	1.1
r_mcbond_other	0.793
r_chiral_restr	0.141
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5898
Nucleic Acid Atoms
Solvent Atoms	733
Heterogen Atoms	86

Software

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