Experiment: 3D4M

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	298	PEG 4000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.634	α = 90
b = 47.634	β = 90
c = 94.592	γ = 90

Symmetry
Space Group	P 41 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	110	CCD	MAR CCD 165 mm		2004-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.431	LNLS	D03B-MX1

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	2.05	42.56	99.8	0.08	6.3	12.3	7349	7295			21.635

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)
	2.05	2.16	99.8		0.294	7.8	11.2	7349

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.05	42.56	7349	7295	340	99.66	0.182	0.18	0.219	RANDOM	21.635

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]
0.68			0.68		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.283
r_dihedral_angle_3_deg	12.891
r_dihedral_angle_1_deg	5.714
r_scangle_it	4.368
r_scbond_it	2.704
r_mcangle_it	1.519
r_angle_refined_deg	1.418
r_mcbond_it	0.906
r_nbtor_refined	0.319
r_nbd_refined	0.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.283
r_dihedral_angle_3_deg	12.891
r_dihedral_angle_1_deg	5.714
r_scangle_it	4.368
r_scbond_it	2.704
r_mcangle_it	1.519
r_angle_refined_deg	1.418
r_mcbond_it	0.906
r_nbtor_refined	0.319
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.207
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	806
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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.