6GZW | pdb_00006gzw

Ferric DtpA from Streptomyces lividans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	Crystals were grown by the vapour diffusion hanging drop method using a ferric protein solution at 13 mg/ml equilibrated against a reservoir consisting of 17-24% PEG 3000 and 50-100 mM sodium citrate, pH 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.118	α = 90
b = 71.032	β = 92.83
c = 78.089	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	PIXEL	DECTRIS EIGER X 16M		2016-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.41	77.99	93.9	0.127	0.141	0.06	0.997	7.8	5.2		118339

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.46	80.4		1.253	1.391	0.593	0.529		5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5MAP	1.41	77.99	112316	5945	93.63	0.1905	0.1891	0.2163	0.1929	RANDOM	15.64

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]
-0.11		-0.17	0.74		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.422
r_dihedral_angle_4_deg	17.662
r_dihedral_angle_3_deg	12.103
r_dihedral_angle_1_deg	6.395
r_angle_refined_deg	1.513
r_angle_other_deg	0.983
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5619
Nucleic Acid Atoms
Solvent Atoms	793
Heterogen Atoms	86

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
EDNA	data reduction