1ZCO

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QR7	CHIMERIC MODEL FROM 1QR7 AND 1FWT
experimental model	PDB	1FWT	CHIMERIC MODEL FROM 1QR7 AND 1FWT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	295	8% Peg 8000, 0.2M ammonium acetate, 0.1M tris-HCl, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.231	α = 90
b = 110.024	β = 90
c = 144.35	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Blue Mirrors	2004-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.25	19.8	99.9	0.126	7.6	4.97	166567	33241			30.1

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	2.25	2.37	100		0.35	3.9	4.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	CHIMERIC MODEL FROM 1QR7 AND 1FWT	2.25	19.8	30722	30722	2519	100	0.186	0.18224	0.19	0.23132	0.24	RANDOM	31.545

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]
0.45			1.72		-2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.654
r_scangle_it	5.405
r_scbond_it	3.68
r_mcangle_it	2.693
r_mcbond_it	1.613
r_angle_refined_deg	1.563
r_angle_other_deg	1.562
r_symmetry_hbond_refined	0.264
r_nbd_other	0.257
r_symmetry_vdw_other	0.253
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.237
r_xyhbond_nbd_refined	0.213
r_chiral_restr	0.093
r_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4112
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	23

Software

Software
Software Name	Purpose
CrystalClear	data collection
CrystalClear	data reduction
MOLREP	phasing
REFMAC	refinement
CrystalClear	data scaling