6LT7 | pdb_00006lt7

Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	277	20% of PEG 3350, 0.2 M ammonium tartrate dibasic, pH 6.6

Crystal Properties
Matthews coefficient	Solvent content
4.25	71.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.168	α = 90
b = 144.168	β = 90
c = 74.223	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS3 6M		2016-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97776	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	50	100	0.187	0.198	0.062	4.1	10.2		47259

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	99.7		0.803	0.857	0.293	0.833		8.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2.7	35.6	44933	2250	99.85	0.1938	0.1916	0.2	0.2385	0.24	RANDOM	62.135

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]
0.96	0.48		0.96		-3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.236
r_dihedral_angle_4_deg	22.92
r_dihedral_angle_3_deg	18
r_dihedral_angle_1_deg	7.894
r_angle_refined_deg	1.813
r_angle_other_deg	1.374
r_chiral_restr	0.099
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.236
r_dihedral_angle_4_deg	22.92
r_dihedral_angle_3_deg	18
r_dihedral_angle_1_deg	7.894
r_angle_refined_deg	1.813
r_angle_other_deg	1.374
r_chiral_restr	0.099
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3671
Nucleic Acid Atoms	2060
Solvent Atoms	271
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXCD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.