3TFH | pdb_00003tfh

DMSP-dependent demethylase from P. ubique - apo

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		6.8	298	25 mM HEPES, 325 mM NaCl, 20% PEG. PEG increased to 30% for cryo, pH 6.8, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.656	α = 90
b = 121.727	β = 101.01
c = 59.648	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	1.9	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	2.1	50	100	0.07	19.2	8.6		43819			34.2

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	2.1	2.18	100		0.201	13		4385

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	2.1	43.51	43813	42744	1066	100	0.1677	0.16607	0.1746	0.23092	0.2403	RANDOM	34.23

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]
1.52		1.43	-1.24		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.328
r_dihedral_angle_4_deg	19.438
r_dihedral_angle_3_deg	16.94
r_dihedral_angle_1_deg	7.319
r_scangle_it	3.663
r_scbond_it	2.413
r_mcangle_it	1.72
r_angle_refined_deg	1.716
r_mcbond_it	1.004
r_angle_other_deg	0.999
r_mcbond_other	0.266
r_chiral_restr	0.111
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5898
Nucleic Acid Atoms
Solvent Atoms	559
Heterogen Atoms	14

Software

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