6ZDW | pdb_00006zdw

Crystal structure of the ribonuclease core of R3B2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291.15	100 mM Hepes/NaOH pH 7.0, 200 mM L-proline and 12% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.91	α = 90
b = 80.759	β = 90
c = 83.783	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-09-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2018-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA
2	SYNCHROTRON	SLS BEAMLINE X10SA	2.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.65	37.95	99.8	0.044	0.048	0.018	0.999	21.8	12.4		62534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	96.9		0.594		9.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	FREE R-VALUE	1.65	37.953	62453	1917	99.725	0.163	0.1621	0.17	0.1824	0.17	40.541

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]
1.397			-3.376		1.978

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.685
r_dihedral_angle_4_deg	26.052
r_dihedral_angle_3_deg	13.614
r_dihedral_angle_1_deg	5.868
r_lrange_it	4.476
r_lrange_other	4.357
r_scangle_other	3.176
r_scangle_it	3.175
r_mcangle_it	3.044
r_mcangle_other	3.044
r_scbond_it	2.537
r_scbond_other	2.532
r_mcbond_it	2.158
r_mcbond_other	2.151
r_angle_other_deg	1.297
r_angle_refined_deg	1.283
r_rigid_bond_restr	1.22
r_nbd_refined	0.197
r_nbd_other	0.187
r_symmetry_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.13
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2282
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
AutoSol	phasing
DIALS	data processing
Aimless	data scaling