3I8Z | pdb_00003i8z

Crystal structure of human chromobox homolog 4 (CBX4)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H91	PDB entry 3H91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	20% Isopropanol, 20% PEG 4000, 0.1 M Na Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.606	α = 90
b = 58.606	β = 90
c = 32.813	γ = 90

Symmetry
Space Group	I 41

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	ADSC QUANTUM 210	Rh-coated Si mirror for vertical focusing		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.97800	CHESS	A1

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	1.5	40	98.4	0.082	17.9	6.9		8902

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)
	1.5	1.55	86.8		0.224		4.6	776

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3H91	1.51	40	8902	425	99.56	0.229	0.228	0.224	0.255	0.2521	RANDOM	21.568

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]
-0.48			-0.48		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.433
r_dihedral_angle_4_deg	16.367
r_dihedral_angle_3_deg	15.416
r_dihedral_angle_1_deg	6.123
r_scangle_it	3.985
r_scbond_it	2.38
r_mcangle_it	1.473
r_angle_refined_deg	1.227
r_mcbond_it	0.954
r_nbtor_refined	0.318
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.197
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	437
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
AMoRE	phasing