5E3B | pdb_00005e3b

Structure of macrodomain protein from Streptomyces coelicolor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M Tris-HCl, 0.29 M sodium chloride, 1.0 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.819	α = 90
b = 103.819	β = 90
c = 33.254	γ = 90

Symmetry
Space Group	P 43 21 2

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 PILATUS 2M		2015-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.976	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	46.43	97.9	0.12	0.043	0.997	11.5	8.6		24097

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	89.5		1.18	0.433	0.67	1.8	8.1	1057

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	2FG1	1.6	46.43	22860	1196	97.76	0.1861	0.1842	0.2233	0.194	RANDOM	19.9

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]
0.41			0.41		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.125
r_dihedral_angle_4_deg	17.252
r_dihedral_angle_3_deg	12.684
r_dihedral_angle_1_deg	6.081
r_mcangle_it	3.289
r_mcbond_it	2.406
r_mcbond_other	2.405
r_angle_refined_deg	2.252
r_angle_other_deg	1.175
r_chiral_restr	0.142
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1128
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	6

Software

Software
Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction