1W77

2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I52	PDB ENTRY 1I52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M HEPES PH 7.5, 0.05 M CADMIUM SULFATE, 1 M SODIUM ACETATE, 0.04 COPPER(II) CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.496	α = 90
b = 74.496	β = 90
c = 223.026	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	160	CCD	ADSC CCD	MIRRORS	2003-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	29.75	99.8	0.05	22.3	16.9		16508

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	2.07	99.4		0.43	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1I52	2	27.95	15674	833	99.8	0.237	0.232	0.349	RANDOM	50.92

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]
0.05	0.02		0.05		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.588
r_dihedral_angle_3_deg	21.323
r_dihedral_angle_4_deg	21.091
r_scangle_it	18.78
r_scbond_it	16.556
r_mcangle_it	11.302
r_dihedral_angle_1_deg	9.782
r_mcbond_it	9.567
r_angle_refined_deg	1.652
r_nbtor_refined	0.33
r_symmetry_vdw_refined	0.324
r_xyhbond_nbd_refined	0.299
r_nbd_refined	0.298
r_symmetry_hbond_refined	0.269
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	1640
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
BEAST	phasing