4MJZ | pdb_00004mjz

2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QW4	PDB entry 3QW4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	295	Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.477	α = 90
b = 115.477	β = 90
c = 152.055	γ = 120

Symmetry
Space Group	P 61 2 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2013-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.75	30	100	0.124	24.2	14.1	16220	16220		-3	53.3

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	2.75	2.8	99.9		0.591	5.3	14.3	797

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 (All)	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 3QW4	2.75	29.1	15330	15330	809	99.83	0.19092	0.19092	0.18817	0.19	0.24602	0.25	RANDOM	46.175

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]
1.55	0.77		1.55		-5.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.304
r_dihedral_angle_4_deg	20.794
r_dihedral_angle_3_deg	13.497
r_long_range_B_refined	6.39
r_long_range_B_other	6.389
r_scangle_other	4.165
r_mcangle_it	3.373
r_mcangle_other	3.372
r_scbond_it	2.592
r_scbond_other	2.589
r_dihedral_angle_1_deg	2.182
r_mcbond_it	2.023
r_mcbond_other	2.012
r_angle_refined_deg	1.628
r_angle_other_deg	1.394
r_chiral_restr	0.082
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4381
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	42

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling