Experiment: 6DCB

Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	277	crystallization solution 0.214 M lithium sulfate, 0.1 M phosphate/citrate, pH 4.2, 17.25% w/v PEG 1,000 mixed 1:2 volume ratio to 10 mg/mL protein:RNA complex solution

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.28	α = 90
b = 118.28	β = 90
c = 78.63	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2018-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.998	62.373	99.9	0.069	0.072	0.999	20.94	12.885		42441			38.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.998	2.05	98.6		0.752	0.784	0.887	3.33	12.448

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5UNA	1.998	62.373	1.37	42437	4243	99.88	0.1619	0.16	0.1666	0.1782	0.1846	47.6433

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.854
f_angle_d	0.956
f_chiral_restr	0.051
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms	775
Solvent Atoms	149
Heterogen Atoms	41

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction