3EP0 | pdb_00003ep0

Methyltransferase domain of human PR domain-containing protein 12

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Purified PRDM12 was crystallized using hanging drop vapor diffusion method at 293K by mixing the protein solution with the reservoir solution containing 19% PEG 2,000 MME, 0.1 M KSCN., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.882	α = 90
b = 34.358	β = 131.09
c = 103.739	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					2008-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1						21829

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 entry 3DAL	2.1		21829	1124	98.88	0.259	0.257	0.2527	0.286	0.2812	RANDOM	24.308

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]
1.76		1.15	-0.14		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.861
r_dihedral_angle_4_deg	25.198
r_dihedral_angle_3_deg	14.024
r_dihedral_angle_1_deg	6.784
r_scangle_it	2.526
r_scbond_it	1.696
r_mcangle_it	1.388
r_angle_refined_deg	1.287
r_mcbond_it	0.848
r_nbtor_refined	0.308
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.166
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1741
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction