3BPW | pdb_00003bpw

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2	293	30% PEG 1000, 100mM Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.902	α = 90
b = 83.582	β = 90
c = 89.793	γ = 90

Symmetry
Space Group	P 21 21 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	DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR	2007-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	50	99.5	0.068	0.068	11.2	4.6		66788

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	95.6		0.394	0.394	2.6	3.5

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	2Q8L	1.7	50	64102	63705	3394	99.4	0.172	0.17	0.17	0.205	0.2	RANDOM	18.72

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]
-0.01			0.22		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.05
r_dihedral_angle_4_deg	20.515
r_dihedral_angle_3_deg	13.739
r_dihedral_angle_1_deg	6.124
r_scangle_it	3.94
r_scbond_it	2.731
r_mcangle_it	1.668
r_angle_refined_deg	1.553
r_mcbond_it	1.079
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.112
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5352
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	60

Software

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