2PNY | pdb_00002pny

Structure of Human Isopentenyl-diphosphate Delta-isomerase 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ICJ	PDB entry 2ICJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.897	α = 90
b = 52.815	β = 90
c = 96.391	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	IMAGE PLATE	RIGAKU RAXIS IV++		2007-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	25	98.7	0.056	36.95	7	24447	24447		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	86.8		0.238	9.6	6.7	2101

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 2ICJ	1.81	24.16	24394	23192	1202	99.93	0.14931	0.14759	0.1533	0.18203	0.1864	RANDOM	13.151

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]
1.29			-0.57		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.426
r_dihedral_angle_4_deg	21.882
r_dihedral_angle_3_deg	12.608
r_dihedral_angle_1_deg	6.317
r_scangle_it	3.597
r_scbond_it	2.517
r_angle_refined_deg	1.618
r_mcangle_it	1.318
r_mcbond_it	0.968
r_nbtor_refined	0.309
r_nbd_refined	0.212
r_metal_ion_refined	0.184
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1931
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing