8Z7K | pdb_00008z7k

Crystal structure of Hemolysin co-regulated protein 1 (Hcp1) VariantB from Burkholderia pseudomallei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	1.5 M ammonium sulfate, 3.75% v/v 2-propanol, 25% glycerol

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.721	α = 90
b = 82.721	β = 90
c = 64.066	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2021-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.999840	NSRRC	TPS 05A

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	1.58	47.76	95.9	0.044	0.048	0.021	1	22.8	9.8		32755			29.5

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	1.58	1.61	71.3		2.013	2.503	1.458	0.258	0.7	4.4

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	1.582	47.76	32753	1558	95.926	0.226	0.2247	0.2243	0.243	0.2426	35.751

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]
-1.131	-0.566		-1.131		3.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.141
r_dihedral_angle_3_deg	11.941
r_lrange_it	9.886
r_lrange_other	9.883
r_scangle_it	6.841
r_scangle_other	6.83
r_dihedral_angle_1_deg	6.656
r_mcangle_it	5.117
r_mcangle_other	5.115
r_scbond_it	4.542
r_scbond_other	4.518
r_dihedral_angle_2_deg	4.286
r_mcbond_it	3.556
r_mcbond_other	3.554
r_angle_refined_deg	1.664
r_angle_other_deg	0.575
r_chiral_restr	0.087
r_gen_planes_other	0.017
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XDS	data scaling
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement