8PNJ

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
experimental model	PDB	5HPQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	1:1 volume ratio of 5 mg/ml protein in 20 mM TRIS-HCl, pH=8, 150 uM NaCl buffer and 0.1M BTP, pH=8.5 0.2M KSCN 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.608	α = 90
b = 105.344	β = 112.484
c = 55.776	γ = 90

Symmetry
Space Group	P 1 21 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 X 9M		2021-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9762	ESRF	ID30B

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	2.35	46.336	97.3	0.959	4.1	3.1		20939			34.2

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	2.35	2.44	85		0.475	1.1

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	2.355	46.336	20919	979	97.234	0.218	0.2148	0.2842	38.122

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]
-0.155		-0.058	2.847		-1.969

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.852
r_dihedral_angle_3_deg	16.804
r_dihedral_angle_6_deg	14.974
r_dihedral_angle_1_deg	7.206
r_lrange_it	6.884
r_lrange_other	6.883
r_scangle_it	4.466
r_scangle_other	4.465
r_mcangle_it	4.416
r_mcangle_other	4.416
r_scbond_it	3.003
r_scbond_other	3.003
r_mcbond_it	2.975
r_mcbond_other	2.97
r_angle_refined_deg	1.451
r_angle_other_deg	0.511
r_symmetry_xyhbond_nbd_other	0.416
r_symmetry_nbd_refined	0.326
r_nbd_other	0.273
r_symmetry_xyhbond_nbd_refined	0.267
r_nbd_refined	0.226
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3087
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	44

Software

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