2I6K | pdb_00002i6k

Crystal structure of human type I IPP isomerase complexed with a substrate analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DHO	PDB ENTRY 2DHO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.2M Magnesium Acetate, 0.1M Sodium Cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.363	α = 80.26
b = 43.074	β = 89.98
c = 70.466	γ = 67.95

Symmetry
Space Group	P 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	RIGAKU RAXIS IV		2005-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	50	94.1	0.098	9.5	5.5		28398

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)
	2	2.07	87		0.464		5.2

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 2DHO	2	20.4	26831	1417	94.28	0.22238	0.22023	0.23	0.26182	0.28	RANDOM	40.404

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]
-0.73	-2.65	0.36	6.03	-0.91	-3.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.663
r_sphericity_free	26.387
r_dihedral_angle_4_deg	17.999
r_dihedral_angle_3_deg	15.591
r_dihedral_angle_1_deg	6.199
r_scangle_it	3.45
r_sphericity_bonded	3.341
r_scbond_it	2.379
r_rigid_bond_restr	1.64
r_mcangle_it	1.557
r_angle_refined_deg	1.293
r_mcbond_it	0.991
r_nbtor_refined	0.301
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.145
r_metal_ion_refined	0.128
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3649
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing