9RVG | pdb_00009rvg

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	Burkholderia thailandensis

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298.5	0.2 M ammonium citrate dibasic 20% w/v PEG 3350 (JCSG+ crystallization screen; Molecular Dimensions Ltd., condition A3).

Crystal Properties
Matthews coefficient	Solvent content
2.1	31.46

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 X 2M		2020-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	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	1.1	39.4	97.4	0.999	15	9.8		103362			14.6

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	1.11	1.23	49.7		0.143	0.6	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.109	39.377	103328	5228	87.663	0.166	0.1653	0.1712	0.1854	0.1974	18.466

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]
-0.749	-0.375		-0.749		2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.899
r_dihedral_angle_3_deg	12.631
r_lrange_other	11.637
r_lrange_it	11.601
r_scangle_it	10.099
r_scangle_other	10.097
r_dihedral_angle_2_deg	9.044
r_scbond_other	7.048
r_scbond_it	7.046
r_mcangle_other	7.016
r_mcangle_it	7.015
r_rigid_bond_restr	5.066
r_mcbond_it	5.04
r_mcbond_other	5.024
r_dihedral_angle_1_deg	4.818
r_angle_refined_deg	1.856
r_angle_other_deg	0.707
r_symmetry_xyhbond_nbd_refined	0.29
r_symmetry_nbd_refined	0.274
r_nbd_refined	0.254
r_nbd_other	0.206
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.177
r_symmetry_nbd_other	0.173
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_other	0.068
r_xyhbond_nbd_other	0.044
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
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	207
Heterogen Atoms	26

Software

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