Experiment: 3ROM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.914	α = 65.21
b = 50.847	β = 83.6
c = 68.617	γ = 82.52

Symmetry
Space Group	P 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	RAYONIX MX-225		2010-05-08	M	SINGLE WAVELENGTH
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97908	SSRF	BL17U

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	2.04	50	97.9	0.069	11.1	3.5		31537

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	2.04	2.12	96.8		0.384		3.4	3108

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	1YH3	2.04	50	31515	1583	97.18	0.1851	0.1829	0.2273	RANDOM	38.506

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]
-0.42	-0.28	-0.67	-0.52	0.75	0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_4_deg	14.892
r_dihedral_angle_3_deg	13.155
r_dihedral_angle_1_deg	5.305
r_scangle_it	2.255
r_scbond_it	1.429
r_angle_refined_deg	1.088
r_angle_other_deg	0.799
r_mcangle_it	0.797
r_mcbond_it	0.401

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_4_deg	14.892
r_dihedral_angle_3_deg	13.155
r_dihedral_angle_1_deg	5.305
r_scangle_it	2.255
r_scbond_it	1.429
r_angle_refined_deg	1.088
r_angle_other_deg	0.799
r_mcangle_it	0.797
r_mcbond_it	0.401
r_mcbond_other	0.096
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4089
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	26

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.