Experiment: 2RJM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	pH 4.6, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.28	α = 90
b = 86.48	β = 104.94
c = 44.41	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 225 mm CCD		2005-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.008	SLS	X06SA

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	18	99.2	0.08	13.77			20955		-3	31.382

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	2	2.02	84.3		0.472	3.2	3.1

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 2RIK	2	18	20955	1071	99.56	0.179	0.176	0.228	RANDOM	30.876

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]
2.68		0.92	-0.95		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.075
r_dihedral_angle_4_deg	20.132
r_dihedral_angle_3_deg	14.739
r_dihedral_angle_1_deg	6.518
r_scangle_it	4.229
r_scbond_it	2.698
r_angle_refined_deg	1.599
r_mcangle_it	1.565
r_mcbond_it	1.019
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.075
r_dihedral_angle_4_deg	20.132
r_dihedral_angle_3_deg	14.739
r_dihedral_angle_1_deg	6.518
r_scangle_it	4.229
r_scbond_it	2.698
r_angle_refined_deg	1.599
r_mcangle_it	1.565
r_mcbond_it	1.019
r_nbtor_refined	0.309
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.205
r_symmetry_hbond_refined	0.201
r_symmetry_vdw_refined	0.171
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2186
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	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.