8PR9 | pdb_00008pr9

The structure of v13Bagel2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293.15	0.1 M HEPES pH 7 30% v/v Jeffamine M-600 pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.518	α = 90
b = 83.515	β = 90
c = 96.946	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 EIGER2 XE 16M		2020-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.35	96.95	100	0.122	0.127	0.035	0.999	8.4	12.8		25904

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	2.35	2.39		100	0.816	0.856	0.254	0.952		11.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.35	63.35	24585	1264	100	0.23937	0.23644	0.25	0.29406	0.3	RANDOM	43.75

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]
2.71			-3.83		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.251
r_long_range_B_other	14.667
r_long_range_B_refined	14.664
r_scangle_other	13.019
r_mcangle_it	9.882
r_mcangle_other	9.88
r_scbond_it	9.848
r_scbond_other	9.847
r_dihedral_angle_1_deg	7.663
r_mcbond_it	7.583
r_mcbond_other	7.583
r_angle_refined_deg	2.348
r_angle_other_deg	0.74
r_chiral_restr	0.099
r_bond_refined_d	0.017
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4904
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
DIALS	data reduction
MOLREP	phasing