4IJD | pdb_00004ijd

Crystal structure of methyltransferase domain of human PR domain-containing protein 9

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	23% PEG 3350, 0.2 M AMMONIUM ACETATE, 0.1 M BisTris pH5.5, vapor diffusion hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.734	α = 90
b = 48.782	β = 100.05
c = 78.713	γ = 90

Symmetry
Space Group	P 1 21 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 315r		2012-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	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	50	99.9	0.093	31.1	6.3	21804	21804			39.1

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	2.2	99.7		0.804		5.2	1089

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.15	36.19	21794	21794	911	99.9	0.1991	0.1991	0.1964	0.264	0.2595	RANDOM	50.9656

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]
0.45		-0.35	0.56		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.447
r_dihedral_angle_4_deg	13.537
r_dihedral_angle_3_deg	13.188
r_dihedral_angle_1_deg	6.84
r_angle_refined_deg	1.195
r_angle_other_deg	0.719
r_chiral_restr	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3275
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data scaling
SOLVE	phasing
Coot	model building