8P6K | pdb_00008p6k

Structure of the hypervariable region of Streptococcus pyogenes M3 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		low resolution model derived from SAD data

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	40% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.474	α = 90
b = 24.107	β = 105.287
c = 78.007	γ = 90

Symmetry
Space Group	C 1 2 1

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		2019-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.969	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.918	75.25	99.7	0.058	0.9	14.8	6.2		21415

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95			1.741	0.5

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	1.918	75.247	21411	1054	99.721	0.232	0.2297	0.24	0.2679	0.27	44.754

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]
-0.913		-2.306	0.838		1.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.115
r_dihedral_angle_4_deg	24.143
r_dihedral_angle_3_deg	15.756
r_lrange_it	9.339
r_lrange_other	9.322
r_scangle_other	8.291
r_scangle_it	8.284
r_scbond_it	5.375
r_scbond_other	5.352
r_mcangle_it	4.957
r_mcangle_other	4.955
r_dihedral_angle_1_deg	4.337
r_mcbond_it	3.936
r_mcbond_other	3.923
r_angle_other_deg	2.269
r_angle_refined_deg	1.44
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.214
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.188
r_nbd_other	0.187
r_nbtor_refined	0.161
r_symmetry_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.095
r_chiral_restr	0.074
r_symmetry_nbtor_other	0.057
r_bond_other_d	0.035
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing