7ESE | pdb_00007ese

The Crystal Structure of human DHFR from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.15M KBr, 30% PEGMME 2000

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.569	α = 90
b = 61.569	β = 90
c = 94.068	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS PILATUS3 6M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.521200	CLSI	08ID-1

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	1.85	47.03	100	0.114	15.9	11.2		16095

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	1.85	1.89			1.086

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	1BOZ	1.85	39.541	15956	791	99.352	0.243	0.2405	0.25	0.285	0.29	32.357

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]
1.431			1.431		-2.861

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.833
r_dihedral_angle_3_deg	17.28
r_dihedral_angle_4_deg	13.944
r_dihedral_angle_1_deg	7.048
r_lrange_it	4.329
r_lrange_other	4.289
r_scangle_it	2.693
r_scangle_other	2.692
r_mcangle_it	2.585
r_mcangle_other	2.584
r_scbond_it	1.61
r_scbond_other	1.609
r_mcbond_it	1.587
r_mcbond_other	1.586
r_angle_refined_deg	1.471
r_angle_other_deg	1.136
r_nbd_other	0.221
r_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.172
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1495
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing