2RH2 | pdb_00002rh2

High Resolution DHFR R-67

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.81	α = 90
b = 67.81	β = 90
c = 51.97	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	Osmic VariMax HF confocal mirrors	2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	0.96	25	96.8	0.1	0.1	27.1	16.3	32858	32858		-3

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)
	0.96	0.99	91.1		0.657	0.657	3.6	6.7	3331

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	1VIE	0.96	25	32858	32858	1776	93.28	0.10387	0.10387	0.10316	0.1	0.11683	0.11	RANDOM	10.397

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]
0.4			0.4		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.053
r_sphericity_free	15.827
r_dihedral_angle_3_deg	11.853
r_dihedral_angle_4_deg	9.956
r_sphericity_bonded	6.735
r_dihedral_angle_1_deg	6.29
r_scangle_it	4.648
r_scbond_it	3.467
r_mcangle_it	3.002
r_mcbond_other	2.353
r_mcbond_it	2.343
r_rigid_bond_restr	2.002
r_angle_refined_deg	1.648
r_angle_other_deg	0.742
r_symmetry_vdw_refined	0.521
r_nbd_refined	0.377
r_symmetry_vdw_other	0.344
r_nbd_other	0.257
r_xyhbond_nbd_refined	0.224
r_nbtor_refined	0.207
r_symmetry_hbond_refined	0.2
r_chiral_restr	0.101
r_nbtor_other	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
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	1082
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	28

Software

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