3QJG | pdb_00003qjg

Epidermin biosynthesis protein EpiD from Staphylococcus aureus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	0.1 M Bis-Tris, 20% PEG-MME-5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.991	α = 90
b = 111.256	β = 97.25
c = 154.569	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 210r		2010-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

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	2.04	45.8	95.3	0.116	8.1	3.9	162302	162302			33.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.04	2.09	74.4		0.481	2.08	2.5	6320

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	1G5Q	2.04	45.8	162164	162164	8177	94.99	0.211	0.211	0.2082	0.2054	0.2626	0.258	RANDOM	32.7319

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]
5.66		0.65	-1.83		-3.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.908
r_dihedral_angle_4_deg	18.385
r_dihedral_angle_3_deg	16.314
r_dihedral_angle_1_deg	6.221
r_scangle_it	3.326
r_scbond_it	2.169
r_angle_refined_deg	1.629
r_mcangle_it	1.289
r_angle_other_deg	0.962
r_mcbond_it	0.755
r_mcbond_other	0.214
r_chiral_restr	0.096
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16396
Nucleic Acid Atoms
Solvent Atoms	1504
Heterogen Atoms	378

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing