3QMD | pdb_00003qmd

Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QMB	PDB 3QMB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1M Hepes pH 7.5, 0.1M MgCl2, 30% PEG550MME., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.653	α = 90
b = 74.688	β = 90
c = 125.769	γ = 90

Symmetry
Space Group	C 2 2 21

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	Rosenbaum-Rock high-resolution double-crystal monochromator	2010-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

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	1.9	50	97.8	0.067	12.7	5.5		11621

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)
	1.9	1.97	88		0.512		4.4	1025

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 3QMB	1.9	32.11	11585	545	97.64	0.2254	0.2246	0.23	0.241	0.25	RANDOM	55.8028

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			-0.24		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.722
r_dihedral_angle_4_deg	22.081
r_dihedral_angle_3_deg	15.918
r_dihedral_angle_1_deg	5.384
r_scangle_it	3.057
r_scbond_it	1.899
r_angle_refined_deg	1.662
r_mcangle_it	1.185
r_mcbond_it	0.649
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.722
r_dihedral_angle_4_deg	22.081
r_dihedral_angle_3_deg	15.918
r_dihedral_angle_1_deg	5.384
r_scangle_it	3.057
r_scbond_it	1.899
r_angle_refined_deg	1.662
r_mcangle_it	1.185
r_mcbond_it	0.649
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	412
Nucleic Acid Atoms	486
Solvent Atoms	26
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
EPICS-based	data collection
data	data collection
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.