4DB9 | pdb_00004db9

Designed Armadillo repeat protein (YIIIM3AIII)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.03	293	1.55 M sodium malonate, pH 8.03, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.92	α = 90
b = 228.88	β = 90
c = 116.53	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MAR scanner 345 mm plate	Helios optical system	2010-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

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	2.4	34.73	100	0.107	5.2	5		65534	4	2	25.3

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	2.4	34.73	65534	3497	99.87	0.21282	0.21106	0.21	0.24579	0.24	RANDOM	21.273

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]
-0.33			-0.16		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.873
r_dihedral_angle_4_deg	18.019
r_dihedral_angle_3_deg	14.951
r_dihedral_angle_1_deg	4.004
r_scangle_it	2.522
r_scbond_it	1.336
r_angle_refined_deg	1.036
r_mcangle_it	0.814
r_mcbond_it	0.401
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.873
r_dihedral_angle_4_deg	18.019
r_dihedral_angle_3_deg	14.951
r_dihedral_angle_1_deg	4.004
r_scangle_it	2.522
r_scbond_it	1.336
r_angle_refined_deg	1.036
r_mcangle_it	0.814
r_mcbond_it	0.401
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9056
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.