3WDF | pdb_00003wdf

Staphylococcus aureus UDG

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	0.1M Hepes sodium pH7.5, 10% 2-propanol, 18% PEG 4000 , EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.408	α = 90
b = 79.494	β = 112.06
c = 62.627	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	ADSC QUANTUM 315		2012-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

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	1.48	58.04	96.6	0.061	26.5	4.3	84916	82029		3

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	1.48	1.53	94.7			4.1

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 (All)	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	2JHQ	1.48	50	80818	77860	4104	96.34	0.14872	0.14872	0.1464	0.1471	0.19232	0.1939	RANDOM	19.369

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]
-0.76		-1.33	0.15		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.307
r_dihedral_angle_4_deg	15.348
r_dihedral_angle_3_deg	13.406
r_scangle_it	6.922
r_dihedral_angle_1_deg	6.336
r_scbond_it	4.636
r_mcangle_it	3.211
r_rigid_bond_restr	2.287
r_mcbond_it	2.034
r_angle_refined_deg	1.643
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3502
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms

Software

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