3TFI | pdb_00003tfi

DMSP-dependent demethylase from P. ubique - with substrate DMSP

X-RAY DIFFRACTION

---

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. Soaked with DMSP, pH 6.8, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.752	α = 90
b = 121.992	β = 100.17
c = 59.373	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	97.4	0.08	23.9	4.5	99295	96714			21.2

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	1.6	1.66	99.8		0.151	10	4.6	9909

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	29.2	98946	94015	2369	97.4	0.13164	0.13034	0.1354	0.18407	0.1848	RANDOM	21.111

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]
0.98		1.3	-0.35		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.701
r_dihedral_angle_4_deg	21.156
r_dihedral_angle_3_deg	15.775
r_dihedral_angle_1_deg	7.528
r_scangle_it	6.987
r_scbond_it	4.94
r_mcangle_it	3.362
r_mcbond_it	2.287
r_rigid_bond_restr	2.132
r_angle_refined_deg	1.968
r_angle_other_deg	1.096
r_mcbond_other	0.822
r_chiral_restr	0.142
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5898
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	30

Software

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