8BWV | pdb_00008bwv

Crystal Structure of SilF Cu(I)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BBZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M potassium sodium tartrate tetrahydrate & 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.297	α = 90
b = 77.297	β = 90
c = 187.69	γ = 90

Symmetry
Space Group	I 21 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		2020-01-15	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	47.275	99.9	0.997	7.8	24.2		28978			43.13

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	2.2	99.4		0.901	1.8	16.5

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	47.275	28978	1427	99.91	0.281	0.2797	0.28	0.2986	0.29	55.098

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]
0.136			0.047		-0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.247
r_dihedral_angle_6_deg	14.509
r_lrange_it	11.526
r_lrange_other	11.525
r_scangle_it	9.57
r_scangle_other	9.568
r_mcangle_it	8.094
r_mcangle_other	8.094
r_dihedral_angle_2_deg	7.036
r_dihedral_angle_1_deg	6.783
r_scbond_it	6.238
r_scbond_other	6.236
r_mcbond_it	5.34
r_mcbond_other	5.334
r_angle_refined_deg	1.44
r_angle_other_deg	0.502
r_symmetry_nbd_refined	0.317
r_nbd_other	0.223
r_metal_ion_refined	0.219
r_nbd_refined	0.208
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.127
r_ncsr_local_group_6	0.124
r_xyhbond_nbd_refined	0.122
r_ncsr_local_group_10	0.116
r_ncsr_local_group_8	0.112
r_ncsr_local_group_11	0.111
r_ncsr_local_group_5	0.109
r_ncsr_local_group_3	0.108
r_ncsr_local_group_9	0.107
r_ncsr_local_group_12	0.106
r_ncsr_local_group_4	0.104
r_ncsr_local_group_13	0.099
r_ncsr_local_group_14	0.088
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_7	0.08
r_ncsr_local_group_15	0.078
r_ncsr_local_group_2	0.071
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3634
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	12

Software

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