8P6J | pdb_00008p6j

Structure of the hypervariable region of Streptococcus pyogenes M3 protein in complex with a collagen peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		native M3 structure obtained through experimental phasing (about to be released)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100mM Tris pH8.5, 8% PEG10k protein 1:1.5 peptide

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.832	α = 87.326
b = 51.503	β = 84.78
c = 80.186	γ = 89.394

Symmetry
Space Group	P 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 EIGER2 XE 16M		2019-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.970	Diamond	I03

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	2.32	79.77	90.2	1	2.1	1.8		35250

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	2.32	2.34			0.3

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	2.324	79.769	19530	947	89.595	0.243	0.2412	0.24	0.2853	0.28	40.861

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]
-0.565	0.43	-0.858	0.796	0.149	-0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.187
r_dihedral_angle_4_deg	24.104
r_dihedral_angle_3_deg	16.857
r_lrange_it	7.01
r_lrange_other	7.009
r_scangle_it	5.457
r_scangle_other	5.456
r_dihedral_angle_1_deg	5.111
r_mcangle_it	4.4
r_mcangle_other	4.4
r_scbond_it	3.491
r_scbond_other	3.49
r_mcbond_it	2.898
r_mcbond_other	2.898
r_angle_refined_deg	1.253
r_angle_other_deg	1.17
r_symmetry_nbd_refined	0.302
r_nbd_other	0.262
r_nbd_refined	0.193
r_symmetry_nbd_other	0.171
r_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.125
r_ncsr_local_group_1	0.115
r_ncsr_local_group_4	0.111
r_ncsr_local_group_3	0.109
r_ncsr_local_group_19	0.106
r_ncsr_local_group_8	0.105
r_ncsr_local_group_12	0.104
r_ncsr_local_group_20	0.098
r_ncsr_local_group_5	0.097
r_ncsr_local_group_15	0.095
r_ncsr_local_group_2	0.094
r_ncsr_local_group_18	0.094
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_6	0.073
r_ncsr_local_group_9	0.066
r_ncsr_local_group_7	0.064
r_ncsr_local_group_16	0.063
r_ncsr_local_group_10	0.053
r_chiral_restr	0.049
r_ncsr_local_group_11	0.044
r_ncsr_local_group_17	0.044
r_ncsr_local_group_21	0.043
r_ncsr_local_group_13	0.042
r_ncsr_local_group_14	0.011
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4011
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

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