4MU1 | pdb_00004mu1

The structure of wt A. thaliana IGPD2 in complex with Mn2+, imidazole, and sulfate at 1.5 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, SITTING DROP	8	290	10% PEG3000, 0.2 M lithium sulfate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.88	α = 90
b = 113.88	β = 90
c = 113.88	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	CCD	ADSC QUANTUM 315	Kirkpatrick Baez bimorph mirror pair	2008-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9507	Diamond	I02

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	1.5	40.26	99.2	0.053	31.8	12.8	40587	40587			12.651

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	1.5	1.54	100		0.676	4	12.2	2956

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	1.5	40.26	40587	38579	2008	99.09	0.15958	0.15806	0.15	0.18832	0.18	RANDOM	22.688

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_free	37.715
r_sphericity_bonded	35.302
r_dihedral_angle_2_deg	30.512
r_rigid_bond_restr	13.947
r_dihedral_angle_4_deg	13.411
r_dihedral_angle_3_deg	10.56
r_scbond_other	9.886
r_scbond_it	9.881
r_scangle_other	9.304
r_long_range_B_refined	7.129
r_long_range_B_other	7.127
r_dihedral_angle_1_deg	6.593
r_mcangle_other	3.399
r_mcangle_it	3.271
r_mcbond_it	3.159
r_mcbond_other	2.848
r_angle_refined_deg	1.571
r_angle_other_deg	0.975
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1439
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	29

Software

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