3UTD | pdb_00003utd

Ec_IspH in complex with 4-oxopentyl diphosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KE8	PDB ENTRY 3KE8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M BIS-TRIS, 0.2 M ammonia sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.11	α = 90
b = 80.39	β = 90
c = 111.24	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	PSI PILATUS 6M		2011-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	1.7	40	99.5	0.059	16.5		69488	69837	2	2

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	1.7	1.8	99.8		0.513	3.4

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	PDB ENTRY 3KE8	1.7	47.73	69521	66045	3476	99.55	0.14884	0.14583	0.1477	0.20607	0.207	RANDOM	26.48

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]
0.48			-1.52		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.246
r_sphericity_free	26.071
r_dihedral_angle_4_deg	20.031
r_dihedral_angle_3_deg	16.426
r_sphericity_bonded	12.923
r_rigid_bond_restr	7.836
r_dihedral_angle_1_deg	5.576
r_angle_refined_deg	2.043
r_angle_other_deg	0.707
r_chiral_restr	0.189
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4773
Nucleic Acid Atoms
Solvent Atoms	515
Heterogen Atoms	44

Software

Software
Software Name	Purpose
RemDAq	data collection
REFMAC	refinement
AC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing