5W9Q | pdb_00005w9q

Zinc finger region of MBD1 in complex with CpG DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HP3	PDB entries 4HP3, 3QMD
experimental model	PDB	3QMD	PDB entries 4HP3, 3QMD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.339	α = 90
b = 27.8	β = 106.52
c = 64.914	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	RAYONIX MX-300		2013-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.979590	CLSI	08ID-1

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	1.8	33.69	99.8	0.046	0.054	0.028	0.998	13.3	3.7		22639

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	1.8	1.84	99.9		0.726	0.848	0.435	0.807		3.7	1337

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 4HP3, 3QMD	1.8	33.69	21331	1306	99.61	0.2277	0.2262	0.234	0.2532	0.2566	thin shells (sftools)	48.642

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]
-1.63		0.36	-4.31		4.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.855
r_dihedral_angle_3_deg	13.875
r_dihedral_angle_4_deg	13.468
r_dihedral_angle_1_deg	6.116
r_angle_refined_deg	1.509
r_mcangle_it	1.393
r_angle_other_deg	1.367
r_mcbond_it	0.836
r_mcbond_other	0.815
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	839
Nucleic Acid Atoms	972
Solvent Atoms	46
Heterogen Atoms	20

Software

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