4PZI | pdb_00004pzi

Zinc finger region of MLL2 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experimental model	Other		structure of isomorphous crystal was solved by molecular replacement using currently unpublished models of same protein and DNA, respectively.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	291	25% PEG-3350, 0.2 M ammonium sulfate, 0.1 M TRIS, pH 8.5, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.736	α = 90
b = 41.005	β = 99.24
c = 55.508	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 315		2013-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	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	2.15	35.36	99.8	0.066	14.3	3.7		8659

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	2.15	2.22	100		1.13	1.4	3.7	729

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MOLECULAR REPLACEMENT	THROUGHOUT	structure of isomorphous crystal was solved by molecular replacement using currently unpublished models of same protein and DNA, respectively.	2.15	34.91	8658	398	99.72	0.228	0.2258	0.2728	0.2585	RANDOM	61.8311

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]
-0.74		0.68	-2.17		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.206
r_dihedral_angle_3_deg	14.005
r_dihedral_angle_4_deg	12.299
r_dihedral_angle_1_deg	5.77
r_mcangle_it	3.962
r_mcbond_it	2.794
r_mcbond_other	2.779
r_angle_refined_deg	1.434
r_angle_other_deg	1.261
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	441
Nucleic Acid Atoms	486
Solvent Atoms	8
Heterogen Atoms	3

Software

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