2RK1 | pdb_00002rk1

DHFR R67 Complexed with NADP and dihydrofolate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RH2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	277	50% 2-methyl-2,4-pentanediol (MPD), 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.804	α = 90
b = 67.804	β = 90
c = 52.201	γ = 90

Symmetry
Space Group	I 41 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	RIGAKU SATURN 92	VARIMAX HF, CONFOCAL MIRRORS	2005-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.26	50	99.6	0.072	14.1	12.4		15838		-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)
	1.26	1.29	96.5		0.499	3	5.4

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	2RH2	1.26	26.22	16692	15838	854	99.67	0.12419	0.12266	0.13	0.15231	0.15	RANDOM, preserved from 2RH2	14.403

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_dihedral_angle_2_deg	34.012
r_sphericity_free	20.897
r_dihedral_angle_3_deg	12.569
r_dihedral_angle_4_deg	11.459
r_sphericity_bonded	6.865
r_scangle_it	6.56
r_dihedral_angle_1_deg	6.219
r_scbond_it	4.852
r_mcangle_it	3.166
r_rigid_bond_restr	2.563
r_mcbond_it	2.499
r_angle_refined_deg	2.121
r_mcbond_other	1.359
r_angle_other_deg	0.87
r_symmetry_vdw_other	0.326
r_nbd_refined	0.298
r_xyhbond_nbd_refined	0.293
r_nbd_other	0.245
r_nbtor_refined	0.225
r_symmetry_vdw_refined	0.163
r_symmetry_hbond_refined	0.141
r_nbtor_other	0.106
r_chiral_restr	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1034
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	85

Software

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