4BGD | pdb_00004bgd

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HIB	PDB ENTRIES 3HIB AND 2OG4
experimental model	PDB	2OG4	PDB ENTRIES 3HIB AND 2OG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		100 MM HEPESNA PH 7.5, 200 MM MGCL2, 32-40% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.77	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.64	α = 90
b = 178.64	β = 90
c = 180.4	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	77	PIXEL	DECTRIS PILATUS 6M		2012-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	3.1	92.2	99.9	0.08	9.8	4.2		63788		6

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	3.1	3.18	100		0.88	1.4	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	SIRAS	THROUGHOUT	PDB ENTRIES 3HIB AND 2OG4	3.1	92.37	60299	3206	99.35	0.21664	0.21373	0.19	0.26993	0.25	RANDOM	121.282

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]
5.73			-7.84		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.919
r_dihedral_angle_4_deg	18.729
r_dihedral_angle_3_deg	17.349
r_mcangle_it	12.739
r_scbond_it	8.782
r_mcbond_it	8.549
r_mcbond_other	8.548
r_dihedral_angle_1_deg	7.085
r_angle_refined_deg	1.477
r_angle_other_deg	0.798
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15663
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
SHARP	phasing