4MU4 | pdb_00004mu4

The form B structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and its substrate, 2R3S-IGP, to 1.41 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	7	290	0.05% PEG2000, 0.4 M succinic acid, pH 7.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.9	α = 90
b = 112.9	β = 90
c = 112.9	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	1.41	65.183	100	0.085	17.7	10.5	47547	47547			12.197

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	1.41	1.45	100		0.849	3.4	10.8	3450

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	1.41	65.183	47547	45244	2303	99.93	0.12495	0.12347	0.13	0.1536	0.15	RANDOM	17.769

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	35.447
r_sphericity_bonded	32.863
r_dihedral_angle_2_deg	31.967
r_dihedral_angle_4_deg	14.888
r_rigid_bond_restr	12.77
r_dihedral_angle_3_deg	10.984
r_scbond_it	7.915
r_scbond_other	7.91
r_scangle_other	7.09
r_long_range_B_other	6.838
r_long_range_B_refined	6.829
r_dihedral_angle_1_deg	6.502
r_mcangle_other	5.416
r_mcangle_it	5.415
r_mcbond_it	5.017
r_mcbond_other	5.01
r_angle_refined_deg	1.497
r_angle_other_deg	0.821
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	1533
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	29

Software

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