2YPQ | pdb_00002ypq

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with tryptophan and tyrosine bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NV8	PDB ENTRY 3NV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 15% V/V GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.777	α = 90
b = 202.777	β = 90
c = 66.747	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	RAXIS			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	39.72	99.2	0.13	7.2	4.06		39770		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.9		0.45	2.4	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NV8	2.76	175.67	37979	1925	98.06	0.18081	0.1773	0.1988	0.24888	0.2541	RANDOM	34.809

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]
-0.23			-0.23		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.614
r_dihedral_angle_4_deg	23.361
r_dihedral_angle_3_deg	22.967
r_dihedral_angle_1_deg	10.675
r_angle_refined_deg	3.348
r_angle_other_deg	1.494
r_chiral_restr	0.171
r_bond_refined_d	0.017
r_gen_planes_refined	0.016
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7029
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
CrystalClear	data scaling