Experiment: 3AML

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M7X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.4	pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.4K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.066	α = 90
b = 124.85	β = 97.29
c = 67.88	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210			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)	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	1.7	50	99.8	0.085	0.085	20.7	3.8	78213	78213

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.78	99.6		0.813	0.813	3.7	3.7	7810

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1M7X	1.7	21.12	74258	3931	99.46	0.14892	0.14643	0.15	0.19592	0.2	RANDOM	23.345

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]
0.1		0.03	-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	14.502
r_dihedral_angle_1_deg	6.401
r_scangle_it	4.973
r_scbond_it	3.424
r_angle_refined_deg	2.246
r_mcangle_it	2.179
r_mcbond_it	1.414
r_chiral_restr	0.187

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	14.502
r_dihedral_angle_1_deg	6.401
r_scangle_it	4.973
r_scbond_it	3.424
r_angle_refined_deg	2.246
r_mcangle_it	2.179
r_mcbond_it	1.414
r_chiral_restr	0.187
r_bond_refined_d	0.029
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5642
Nucleic Acid Atoms
Solvent Atoms	688
Heterogen Atoms	235

Software

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

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.