7DP5 | pdb_00007dp5

Crystal structure of mutant V45A Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HVY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	273	0.1 M HEPES, pH 7.5, 0.9 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.281	α = 90
b = 81.281	β = 90
c = 105.24	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	RAYONIX MX300HE	DCM	2013-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.6	30	99.9	0.043	0.049	0.023	0.999	34.73	4.6		53607

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66			0.485	0.552	0.259	0.809	3.61	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1HVY	1.6	23.754	53565	2722	99.814	0.172	0.1709	0.18	0.1894	0.2	22.215

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]
0.129	0.065		0.129		-0.419

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.531
r_dihedral_angle_4_deg	17.941
r_dihedral_angle_3_deg	11.472
r_dihedral_angle_1_deg	6.327
r_lrange_it	5.116
r_lrange_other	5.03
r_scangle_it	2.798
r_scangle_other	2.798
r_mcangle_it	2.157
r_mcangle_other	2.156
r_scbond_it	1.736
r_scbond_other	1.735
r_angle_other_deg	1.346
r_mcbond_it	1.309
r_angle_refined_deg	1.306
r_mcbond_other	1.304
r_xyhbond_nbd_refined	0.249
r_nbd_refined	0.229
r_nbd_other	0.223
r_symmetry_xyhbond_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.148
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.061
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2296
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	73

Software

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