8PNH | pdb_00008pnh

Chorismate mutase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8CQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8 storage buffer and crystallization solution containing 0.07 M NPS (0.023 M solidum nitrate, 0.023 M disodium hydrogen phosphate and 0.023 M ammonium sulfate) 9% v/w PEG20K 19% v/w 500MME 0.01 M Imidazole 0.008 M phenylpyruvate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.511	α = 90
b = 74.282	β = 90
c = 129.352	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.976	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	1.9	41.51	97.8	0.996	10.6	3.1		31515			36.6

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	1.9	1.94	95.8		0.364	0.8	2.5

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	1.9	37.318	31468	1623	97.18	0.215	0.2127	0.22	0.2667	0.27	41.46

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]
0.439			0.212		-0.651

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.027
r_dihedral_angle_3_deg	16.687
r_dihedral_angle_6_deg	15.092
r_lrange_other	7.797
r_lrange_it	7.793
r_dihedral_angle_1_deg	6.263
r_scangle_other	6.12
r_scangle_it	6.114
r_dihedral_angle_other_3_deg	5.7
r_mcangle_other	4.581
r_mcangle_it	4.579
r_scbond_other	4.142
r_scbond_it	4.138
r_mcbond_it	3.438
r_mcbond_other	3.432
r_angle_refined_deg	1.388
r_angle_other_deg	0.468
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.174
r_nbd_other	0.173
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.039
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2994
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	33

Software

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