9GF2 | pdb_00009gf2

CC-Hex-hen2 variant peptide with Hendecad repeat substitution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium Acetate, 0.1 M BIS-Tris, pH 5.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.563	α = 90
b = 58.157	β = 90
c = 59.258	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 EIGER2 XE 16M		2021-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.099	48.61	100	0.011	0.015	0.011	1	26.6	1.8		10287

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	2.1	2.16	99.9		0.071	0.101	0.071	0.986	4.7	1.9

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	AB INITIO PHASING	FREE R-VALUE	2.099	48.61	10287	536	99.99	0.227	0.2236	0.2249	0.2925	0.2307	53.037

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]
0.056			-0.433		0.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.335
r_lrange_other	16.743
r_lrange_it	16.738
r_scangle_it	14.498
r_scangle_other	14.49
r_dihedral_angle_6_deg	13.397
r_mcangle_it	11.806
r_mcangle_other	11.8
r_scbond_it	10.345
r_scbond_other	10.338
r_mcbond_other	9.172
r_mcbond_it	9.165
r_dihedral_angle_1_deg	7.216
r_angle_refined_deg	2.694
r_angle_other_deg	0.911
r_symmetry_xyhbond_nbd_refined	0.437
r_nbd_other	0.323
r_nbd_refined	0.242
r_symmetry_nbd_refined	0.227
r_xyhbond_nbd_refined	0.221
r_symmetry_xyhbond_nbd_other	0.219
r_nbtor_refined	0.201
r_symmetry_nbd_other	0.196
r_ncsr_local_group_7	0.178
r_ncsr_local_group_10	0.174
r_ncsr_local_group_9	0.172
r_ncsr_local_group_6	0.163
r_ncsr_local_group_13	0.163
r_ncsr_local_group_14	0.158
r_ncsr_local_group_3	0.157
r_ncsr_local_group_2	0.155
r_ncsr_local_group_1	0.153
r_ncsr_local_group_8	0.148
r_ncsr_local_group_4	0.147
r_ncsr_local_group_5	0.145
r_ncsr_local_group_11	0.142
r_ncsr_local_group_15	0.14
r_chiral_restr	0.136
r_ncsr_local_group_12	0.128
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1372
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	16

Software

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