2RB4

Crystal structure of the Helicase domain of human DDX25 RNA helicase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M Bis-Tris propane, 2.5 M Ammonium sulfate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.31	α = 90
b = 70.31	β = 90
c = 187.12	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	IMAGE PLATE	MACSCIENCE	mirrors	2006-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.95373	BESSY	14.2

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	2.8	20		0.107	15.65	8.8	12185	12185			64.1

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)
	2.8	2.9	100		0.82	2.59	9.1	1184

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	PDB entry 1FUK	2.8	19.44	11208	11208	974	100	0.23607	0.23607	0.23338	0.28	0.26655	0.29	RANDOM	82.026

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]
-0.22			-0.22		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.818
r_dihedral_angle_4_deg	22.595
r_dihedral_angle_3_deg	18.195
r_dihedral_angle_1_deg	6.446
r_scangle_it	1.573
r_angle_refined_deg	1.244
r_scbond_it	0.926
r_mcangle_it	0.721
r_mcbond_it	0.389
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2623
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing