7B21 | pdb_00007b21

The X183 domain from Cellvibrio japonicus Cbp2D

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES pH 7.5, 20% w/v PEG 4000, 10% w/v propan-2-ol

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.509	α = 90
b = 55.376	β = 90
c = 55.855	γ = 90

Symmetry
Space Group	P 2 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	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.2	55.85	100	0.05	0.06	0.033	0.997	48.3	6		28435

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	1.2	1.22			0.088	0.105	0.057	0.99		6

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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.2	39.356	28390	1404	99.923	0.113	0.1124	0.1125	0.1279	0.128	11.724

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]
-0.098			0.262		-0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.673
r_dihedral_angle_4_deg	21.522
r_dihedral_angle_other_3_deg	16.384
r_dihedral_angle_3_deg	9.989
r_mcbond_it	9.275
r_mcbond_other	9.274
r_rigid_bond_restr	8.942
r_mcangle_it	8.121
r_mcangle_other	8.117
r_dihedral_angle_1_deg	6.215
r_lrange_it	5.995
r_lrange_other	5.995
r_scangle_it	2.484
r_scangle_other	2.482
r_scbond_it	2.073
r_scbond_other	2.073
r_angle_refined_deg	1.945
r_angle_other_deg	1.852
r_symmetry_xyhbond_nbd_refined	0.308
r_nbd_refined	0.263
r_symmetry_nbd_refined	0.252
r_nbd_other	0.207
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.18
r_metal_ion_refined	0.117
r_chiral_restr	0.114
r_xyhbond_nbd_refined	0.098
r_symmetry_nbtor_other	0.092
r_gen_planes_other	0.026
r_bond_refined_d	0.022
r_gen_planes_refined	0.021
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	715
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
SHELXDE	phasing