7CCM | pdb_00007ccm

Crystal structure of selenomethionine-derived human BFK

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	0.1 M Bis-Tris pH 5.5, 28% PEG 3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.156	α = 90
b = 116.156	β = 90
c = 27.679	γ = 120

Symmetry
Space Group	P 32

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 EIGER X 9M		2019-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97918	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.45	50	99.1	0.071	0.997	12.32	3.1		15406

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.49	90.9		0.784	0.803	1.06	2

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	FREE R-VALUE	2.45	38.05	12693	629	82.561	0.214	0.2124	0.2174	0.2538	0.2502	39.143

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]
0.183	0.092		0.183		-0.595

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.756
r_dihedral_angle_3_deg	13.018
r_dihedral_angle_4_deg	8.221
r_dihedral_angle_1_deg	3.639
r_lrange_it	3.199
r_lrange_other	3.199
r_scangle_it	2.146
r_scangle_other	2.146
r_mcangle_it	1.723
r_mcangle_other	1.722
r_scbond_it	1.378
r_scbond_other	1.378
r_angle_refined_deg	1.119
r_angle_other_deg	1.056
r_mcbond_it	0.964
r_mcbond_other	0.964
r_nbd_refined	0.159
r_symmetry_nbd_other	0.154
r_nbd_other	0.136
r_nbtor_refined	0.133
r_xyhbond_nbd_refined	0.105
r_symmetry_nbd_refined	0.084
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_refined	0.071
r_chiral_restr	0.024
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3310
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing