6BW3

Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.979	α = 90
b = 59.822	β = 94.55
c = 101.773	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN A200		2017-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	2.2	46.95	99.4	0.099	0.114	0.056	0.99	14.3	4.1		46303

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	2.2	2.27	98.4		0.991	1.141	0.559	0.681		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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2xu7	2.2	46.95	44059	2217	99.3	0.21671	0.21521	0.24594	RANDOM	43.608

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]
0.05		0.43	-0.82		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.885
r_dihedral_angle_3_deg	14.216
r_dihedral_angle_4_deg	12.841
r_dihedral_angle_1_deg	6.931
r_long_range_B_refined	3.312
r_long_range_B_other	3.305
r_angle_refined_deg	1.476
r_angle_other_deg	0.965
r_mcangle_it	0.94
r_mcangle_other	0.94
r_scangle_other	0.695
r_mcbond_it	0.536
r_mcbond_other	0.536
r_scbond_it	0.417
r_scbond_other	0.417
r_chiral_restr	0.09
r_bond_refined_d	0.011
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5841
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing