7PPP | pdb_00007ppp

Crystal structure of ZAD-domain of ZNF_276 protein from rabbit.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.1M bicine pH 8.5, PEG 20000 5%, dextrane sulfate 5%

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.94	α = 90
b = 82.94	β = 90
c = 134.32	γ = 120

Symmetry
Space Group	P 63 2 2

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		2021-06-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313, 1.282	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.9	49.1	98.8	0.052	0.054	0.999	25.91	11.043		6460			108.322

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	99.8		1.363	1.42	0.744	1.87	11.586

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.9	49.1	6459	609	98.777	0.295	0.2896	0.29	0.3399	0.34	RANDOM	99.154

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]
0.526	0.263		0.526		-1.706

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.911
r_dihedral_angle_3_deg	23.432
r_dihedral_angle_4_deg	17.116
r_lrange_it	13.492
r_lrange_other	13.481
r_scangle_it	11.897
r_scangle_other	11.89
r_mcangle_it	11.596
r_mcangle_other	11.588
r_dihedral_angle_1_deg	10.503
r_scbond_it	9.42
r_scbond_other	9.413
r_mcbond_other	7.766
r_mcbond_it	7.761
r_angle_refined_deg	2.922
r_angle_other_deg	1.467
r_xyhbond_nbd_refined	0.209
r_ncsr_local_group_1	0.202
r_nbd_other	0.165
r_nbd_refined	0.161
r_nbtor_refined	0.137
r_chiral_restr	0.123
r_symmetry_nbd_other	0.12
r_symmetry_nbtor_other	0.074
r_symmetry_nbd_refined	0.074
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	977
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing
PDB_EXTRACT	data extraction