8PNI

Chorismate mutase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	1:3 volume ratio of 8 mg/mL protein in 20 mM Bis-Tris, pH 6.5 storage buffer and 0.2 M ammonium citrate dibasic 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.445	α = 90
b = 48.445	β = 90
c = 113.364	γ = 120

Symmetry
Space Group	P 32

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 2M		2020-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	1.21	39.35	97.4	0.999	15	9.8		88399

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	1.21	1.23	79.8		0.507	1.5	7.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.21	39.35	88367	4283	97.353	0.144	0.1429	0.1706	20.706

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]
0.135	0.067		0.135		-0.437

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	22.211
r_dihedral_angle_6_deg	16.322
r_dihedral_angle_3_deg	14.381
r_dihedral_angle_2_deg	13.036
r_scangle_it	11.408
r_scangle_other	11.406
r_scbond_other	10.39
r_scbond_it	10.383
r_lrange_other	9.475
r_lrange_it	9.465
r_mcangle_it	7.406
r_mcangle_other	7.404
r_mcbond_it	6.818
r_mcbond_other	6.811
r_dihedral_angle_1_deg	4.62
r_angle_refined_deg	1.472
r_angle_other_deg	0.559
r_nbd_refined	0.251
r_symmetry_xyhbond_nbd_refined	0.223
r_symmetry_nbd_refined	0.22
r_nbd_other	0.207
r_xyhbond_nbd_refined	0.177
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.172
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.066
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2442
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	26

Software

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