Experiment: 3DJX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.585	α = 90
b = 59.016	β = 90
c = 82.247	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2007-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8088	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.69	27.775	98.1	0.059	14.1	3.9	26589	26554		-3	16.968

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	98.7		0.445	3.4	3.8	4382

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1R5D	1.69	27.77	25228	1326	97.45	0.17036	0.16862	0.20428	RANDOM	14.364

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]
-0.07			-0.1		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.825
r_dihedral_angle_3_deg	12.498
r_dihedral_angle_4_deg	11.941
r_dihedral_angle_1_deg	5.844
r_scangle_it	2.907
r_scbond_it	1.862
r_angle_refined_deg	1.284
r_mcangle_it	1.14
r_mcbond_it	0.685
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.825
r_dihedral_angle_3_deg	12.498
r_dihedral_angle_4_deg	11.941
r_dihedral_angle_1_deg	5.844
r_scangle_it	2.907
r_scbond_it	1.862
r_angle_refined_deg	1.284
r_mcangle_it	1.14
r_mcbond_it	0.685
r_nbtor_refined	0.293
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1882
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.