2H6Q | pdb_00002h6q

Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERJ	PDB ENTRY 1ERJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.257	α = 90
b = 46.336	β = 116.72
c = 111.405	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	Si(111)	2006-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C		APS	24-ID-C

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	1.88	33.2	99.4	0.091	19.8	6.9	50232	46407	2	2	25.7

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	1.88	1.95	95.1		0.271	6.63	5.4	4776

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 ENTRY 1ERJ	1.87	33.2	2	48890	46407	2483	96.18	0.17	0.15348	0.1518	0.15	0.18464	0.19	RANDOM	17.917

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]
-0.88		-0.68	-0.81		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.906
r_dihedral_angle_4_deg	17.19
r_dihedral_angle_3_deg	12.423
r_dihedral_angle_1_deg	7.062
r_scangle_it	3.414
r_scbond_it	2.208
r_angle_refined_deg	1.373
r_mcangle_it	1.207
r_mcbond_it	0.782
r_nbtor_refined	0.301
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4826
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
MOLREP	phasing