Experiment: 2D31

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10.5	293	CAPS, PEG8000, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.641	α = 90
b = 127.807	β = 90
c = 72.58	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	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	3.2	50	83.8	0.09	6.2	4.9		12897		1

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)
	3.2	3.31	77.7		0.325	2.1	4	1162

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MHE	3.2	50	11791	896	83.8	0.2394	0.2347	0.29835	RANDOM	45.459

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]
-0.09			-0.62		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.906
r_dihedral_angle_3_deg	22.671
r_dihedral_angle_4_deg	19.242
r_dihedral_angle_1_deg	6.528
r_angle_refined_deg	1.363
r_symmetry_vdw_refined	0.335
r_nbtor_refined	0.31
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.234
r_xyhbond_nbd_refined	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.906
r_dihedral_angle_3_deg	22.671
r_dihedral_angle_4_deg	19.242
r_dihedral_angle_1_deg	6.528
r_angle_refined_deg	1.363
r_symmetry_vdw_refined	0.335
r_nbtor_refined	0.31
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.234
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.094
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6124
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.