8BBZ | pdb_00008bbz

Crystal Structure of SilF (apo form)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.01 M Zinc sulphate heptahydrate, 0.1 M MES pH 6.5, 25% v/v PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.47	α = 90
b = 109.47	β = 90
c = 84.59	γ = 120

Symmetry
Space Group	P 65 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 PILATUS3 6M		2019-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.999	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	47.402	98.87	1	15.1	36.9		15531

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.279			0.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2VB2	2.2	47.402	15531	802	98.898	0.217	0.2147	0.22	0.2596	0.26	50.07

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]
-0.013	-0.007		-0.013		0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.225
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	14.123
r_lrange_other	11.553
r_lrange_it	11.552
r_scangle_it	9.083
r_scangle_other	9.079
r_dihedral_angle_1_deg	6.785
r_mcangle_it	6.079
r_mcangle_other	6.077
r_scbond_it	6.01
r_scbond_other	6.007
r_mcbond_it	4.314
r_mcbond_other	4.313
r_angle_other_deg	2.336
r_angle_refined_deg	1.558
r_symmetry_nbd_refined	0.418
r_nbd_other	0.27
r_symmetry_metal_ion_refined	0.26
r_nbd_refined	0.214
r_symmetry_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.162
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.064
r_bond_other_d	0.035
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1782
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing