4MU0 | pdb_00004mu0

The structure of wt A. thaliana IGPD2 in complex with Mn2+ and 1,2,4-triazole at 1.3 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F1D	PDB ENTRY 2F1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	290	30% PEG200, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.13	α = 90
b = 113.13	β = 90
c = 113.13	γ = 90

Symmetry
Space Group	P 4 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	100	PIXEL	DECTRIS PILATUS 6M	two K-B pairs of bimorph type mirrors	2011-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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	1.3	50.59	100	0.053	25.2	12.3	61097	61097			12.36

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	1.3	1.33	99.9		0.762	3.5	12.5	4421

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 2F1D	1.3	50.59	61097	58015	3072	99.88	0.13049	0.12956	0.13	0.14806	0.14	RANDOM	19.128

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	35.322
r_dihedral_angle_2_deg	30.94
r_sphericity_free	25.551
r_dihedral_angle_4_deg	15.992
r_rigid_bond_restr	13.402
r_dihedral_angle_3_deg	10.415
r_scbond_other	9.539
r_scbond_it	9.533
r_dihedral_angle_1_deg	6.604
r_scangle_other	6.07
r_long_range_B_other	5.637
r_long_range_B_refined	5.635
r_mcangle_other	2.027
r_mcangle_it	1.931
r_mcbond_it	1.747
r_angle_refined_deg	1.525
r_mcbond_other	1.52
r_angle_other_deg	0.852
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1439
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	24

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling